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The Cystic Fibrosis Story / CFTR

The CFTR protein in 3D, from four published structures

Research, not medical advice

CFTR is a human protein, and variants of it are linked to cystic fibrosis. Here are four published structures of it, each drawn as a smooth tube through the position of one atom in every amino acid it places. Turn them, switch between them, and see where amino acid 508 sits, and where it is absent in the two structures of CFTR with F508del (8EIQ and 8EJ1).

The positions of the points come from published structure files, not from a drawing; the tube that joins them is ours. What a structure cannot show is listed below.

T2 Receipt · Cryo-EM Coordinate Pin (6MSM, 5UAK, 8EIQ, 8EJ1) & GitHub Proof

Primary Sources: RCSB PDB entries 6MSM, 5UAK, 8EIQ, 8EJ1 and UniProt P13569 (Zhang & Chen Cell 2017/2018; Fiedorczuk & Chen Nature 2022).

Lock SHA-256: 568cd8430b9878c8ea8202f3e213b15a0d9d03dce2fec32878ea07f85cc02492 (data/cftr.lock.json, research commit 7490af57).

GitHub Proof: cf-research/tools/cftr-model ↗ · data/cftr.lock.json ↗

Turn it yourself

The 3D view needs JavaScript and WebGL2. It has not started. The facts it shows are also written out as text and in the table further down this page.

Track A · Interactive Kinetics

Interactive Allosteric Rescue and Nonsense Readthrough Kinetics Simulator

Simulating allosteric corrector rescue and nonsense readthrough kinetics for Class I mutations (G542X and W1282X) alongside Cryo-EM 3D coordinates: SMG1-mediated transcript rescue, engineered suppressor tRNA opal readthrough, and ERAD escape curves.

60%

Rescues premature termination transcripts from UPF1-phospho decay, expanding steady-state mRNA pools.

9.0%

Engineered tRNA inserts cognate amino acid at premature UGA stop codon. Optimal window: 6–10% to prevent proteotoxicity.

4.8x

Transmembrane clamp (TMD1/TMD2) accelerates post-translational folding, rescuing channels from the 1,281-aa ERAD trap.

Predicted Transepithelial Conductance (ΔIsc)
10.4%
Model Threshold Reached (≥ 10.0% WT Current)
Salvaged mRNA 62.4%
Effective Readthrough 9.4%
Proteome Safety (TRSS) 96.2 / 100
ERAD Escape Rate 72.0%
OPTIMAL SAFETY WINDOW
G542X (c.1624G>T)

Exon 12 · UGA G (+4 flanking context)

541 aa translated (missing 939 aa) · Ribosome Quality Control (RQC) & Proteasomal Cleavage

Δd(6MSM→5UAK) = 8.52 Å · Δd(6MSM→8EIQ) = 1.93 Å

Aborts at residue 541 before NBD1 alpha-core; correctors cannot bind without prior readthrough (cotranslational RQC clearance).

Clinical & Discovery Presets:

Investigational biophysical model based on PDB 6MSM/8EIQ Cryo-EM coordinates, RefSeq NM_000492.4, and Manfredi et al. (Biochemistry 2025). Research simulation only; not clinical guidance.

Biophysical Mechanism · Channel Dynamics

Interactive CFTR Channel Gating and Trafficking Schematic

Compare normal apical membrane trafficking, PKA phosphorylation, and ATP-dependent chloride conductance against F508del domain misfolding and endoplasmic reticulum-associated degradation (ERAD).

Biophysical channel gating & trafficking comparison: apical ion transport versus ubiquitin-proteasome degradation. Schematic, not a structure.

Track A · Curative Gene Editing

Interactive Prime Editing Feasibility Explorer (F508del & W1282X)

In-silico biophysical feasibility modeling for prime editing pegRNA primer binding site (PBS) thermodynamics, reverse transcriptase template (RTT) length constraints, PE3/PE3b nicking strategies, and dual-vector delivery packaging limits.

Biophysical prime editing flap resolution & delivery packaging model: in-silico pegRNA thermodynamics and dual-vector constraints. Schematic, not a structure.

Track A · Curative Biophysics

Interactive NBD1 Thermal Unfolding (ΔTm) & Domain-Interface (ΔΔG) Explorer

Differential scanning calorimetry (DSC) unfolding transitions, ΔΔG coupling with ICL4, and corrector rescue energetics grounded in PDB 6MSM and 8EIQ.

Target Mutation
Corrector Regimen
DSC Sigmoidal Denaturation & Energetics Model
NBD1 Thermal Denaturation and Interface Free Energy Diagram DSC thermal unfolding curve and domain interface energetic bars.
Melting Temperature (Tm) -- Unfolded at 37°C: --%
Total Coupled ΔΔG -- Conformational Barrier
Apical Trafficking (Band C) -- Endoplasmic Reticulum Fate
Single-Channel Open Probability (Po) -- Wild-Type reference ~0.38
Rare Allele Theratyping & Organoid FIS AUC0-120 min (T-0201) AUC: ~1,850 · EC50: 0.12 μM · ETI Modulator Eligible (NCT04043806) Therapeutic modality routing: Modulator vs HIT-CF Triple (NCT06468527) vs Genetic Cargo (NCT05248230 / NCT05668741)

Research, not medical advice. Computational biophysical model based on DSC melting profiles and structural interfaces (PDB 6MSM, 8EIQ). NCT04043806, NCT06468527. Schematic, not a structure.

Track A · MWC Allosteric Thermodynamics (T-0231)

Interactive CFTR Potentiator & Triple-Corrector Cooperative Allosteric Gating Cycle Explorer

Monod-Wyman-Changeux (MWC) 2N microstate grand partition function coupling Cryo-EM pockets TMD1 (VX-661), TMD2 (VX-445 / VX-121), and the TM4/5/8 lipid-facing gating hinge (VX-770 / VX-561) in PDB 8EIQ and 6MSM.

CFTR Genotype
Combination Modulator Regimen
1.0x
2N-State MWC Thermodynamic Cycle & Cryo-EM Pocket Coupling (PDB 8EIQ)
MWC Allosteric Gating Dose-Response and Cryo-EM 8EIQ Pocket Coupling Diagram Left panel: open probability vs modulator concentration multiplier. Right panel: cooperative stabilization across TMD1, TMD2, and TM4/5/8 hinge.
Treated Open Probability (P_open) -- Basal: --
Single-Channel Current (I_Cl) -- Net affinity α_eff: --
Thermodynamic Synergy (S_123) -- Z_O = -- · Z_C = --
Predicted Sweat Cl- Shift (ΔSwCl) -- Clinical benchmark: --

Research, not medical advice. Computational biophysical model based on MWC grand partition functions and Cryo-EM coordinates (PDB 8EIQ, 6MSM; Fiedorczuk & Chen, Science 2022, DOI 10.1126/science.ade2216). ClinicalTrials.gov data (NCT04043806, NCT06468527) are used with attribution to the U.S. National Library of Medicine (NLM). Schematic, not a structure.

Track A · Biophysical Gating & Cooperativity (T-0280)

Interactive CFTR Gating Potentiator Allosteric Cooperativity & Free-Energy Coupling Simulator

In plain words: Some CFTR mutations leave the channel trapped shut like a stiff spring. Potentiators wedge into the channel to hold it open longer. When two different potentiators bind at once, their combined grip can release trapped channels far more than either medicine acting alone.

Thermodynamic mutant cycle analysis and free-energy coupling (ΔΔGopen = -RT ln(Keq / Keq,0)) between TM8 lipid-hinge potentiators (Ivacaftor / Deutivacaftor) and NBD-TMD interface boosters (GLPG1837) across Class III (G551D, G1244E, S549N) and Class IV (R117H) gating alleles.

CFTR Genotype & Gating Allele
Primary Site 1 Potentiator (TM8 Hinge)
100 nM
Dual-Potentiator Allosteric Cooperativity
Thermodynamic Mutant Cycle & Cryo-EM Potentiator Coupling (PDB 8EIQ, 8EJ1)
CFTR Potentiator Allosteric Cooperativity & Free-Energy Coupling Diagram Left panel: dose-response open probability vs concentration. Right panel: four-state thermodynamic cycle and free-energy coupling linkage.
Open Probability (P_open) -- Basal: --
Macroscopic Cl- Current (I_Cl) -- Basal: --
Free-Energy Coupling (ΔΔG) -- Allosteric ratio α: --
Open Burst Duration (τ_burst) -- Basal: --

Research, not medical advice. Computational thermodynamic mutant cycle model grounded in human Cryo-EM coordinates (PDB 8EIQ, 8EJ1, 6MSM; Van Goor et al., PNAS 2009, DOI 10.1073/pnas.0904709106; Liu et al., Science 2019, DOI 10.1126/science.aaw7611; Yeh et al., J Gen Physiol 2020, DOI 10.1085/jgp.202012676; Zhang et al., Cell 2021, DOI 10.1016/j.cell.2021.02.012). ClinicalTrials.gov data (NCT00909532) are cited with attribution to the U.S. National Library of Medicine (NLM): ClinicalTrials.gov does not evaluate safety or efficacy; listing on the registry does not denote government endorsement. Schematic, not a structure.

Track A · Cryo-EM Nonsense Truncation (T-0238)

Interactive CFTR Truncation 3D Backbone Trace & Cryptic Domain Stability Explorer

Visualizing 3D Cα residue backbone truncation, steric residue loss, and thermal unfolding profiles for W1282X, G542X, and R1162X grounded in human Cryo-EM coordinates (PDB 6MSM, 5UAK, 8EIQ).

Nonsense Truncation Variant
Allosteric Modulator Co-Treatment
CFTR Cα Backbone Trace & Nonsense Stop Codon Position (PDB 6MSM)
CFTR Truncation 3D Backbone Trace and Domain Stability Diagram Diagram showing synthesized versus deleted CFTR domains, Cryo-EM C-alpha coordinates, and allosteric stabilization distances.
Synthesized Polypeptide Length -- PDB 6MSM Cα: --
Exposed Hydrophobic SASA -- Solvent-accessible surface area
Thermal Unfolding Shift (ΔTm) -- Differential scanning fluorimetry
Predicted Degradation / Export Fate -- ERAD quality control vs Golgi escape

Research, not medical advice. Computational structural analysis grounded in human CFTR Cryo-EM coordinates (PDB 6MSM, 5UAK, 8EIQ), NCT04135495, and Manfredi et al. (Biochemistry 2025, DOI: 10.1021/acs.biochem.5c00590). Schematic, not a structure.

Track B · Sequence Windows & Foundation Models (T-0268)

Interactive CFTR Sequence-Window & Open-Source Foundation Model Explorer

Exploring RefSeq NM_000492.4 protospacer windows (SpCas9 / SpG / SpRY), ABE8e bystander deamination, cryptic splice ASO thermodynamics, and ESM-2 / ThermoMPNN zero-shot biophysical disentanglement across CFTR mutation classes.

CFTR Allele (RefSeq NM_000492.4)
Cas9 Variant & PAM Motif
Target & Strategy --

Sequence-guided therapeutic modality

Window Efficiency / ΔΔG° --

Catalytic window or folding shift

Bystander Risk / Classification --

Off-target collision or mechanistic phenotype

Payload Audit / Processing --

TLR9 CpG dinucleotides or Band C Golgi export

Research, not medical advice. Computational model based on RefSeq NM_000492.4, ESM-2 (Lin et al., Science 2023, DOI 10.1126/science.ade2574), ProteinMPNN (Dauparas et al., Science 2022, DOI 10.1126/science.add2187), and Cryo-EM coordinates (PDB 5UAK, 6MSM, 8EIQ). ClinicalTrials.gov data (NCT05248230, NCT05668741, NCT04684641, NCT04135495) are used with attribution to the U.S. National Library of Medicine (NLM); ClinicalTrials.gov does not evaluate safety or efficacy. The lab does not assess efficacy or recommend treatments. Schematic, not a structure.

Track B · Deep Intronic Splice Foundation & ASO Rescue (T-0274)

Interactive Deep Intronic Splice Foundation Model & Pseudoexon Rescue Simulator

Evaluating SpliceAI and Evo-2 cryptic splice donor/acceptor activation, in-frame pseudoexon inclusion, and steric-blocking antisense oligonucleotide (ASO) rescue kinetics across non-coding CFTR alleles.

Intronic CFTR Allele
Antisense Oligonucleotide Chemistry
ASO Titration Concentration
60 nM
SpliceAI & Evo-2 Foundation Scores --

Splice site gain/loss and pathogenicity

ASO Hybridization Net Affinity --

Thermodynamic ΔG°, Tm, and estimated EC50

Canonical Transcript Fraction (f_WT) --

Normal mature mRNA restoration

Apical Chloride Transport (% WT) --

Electrophysiological function vs curative threshold

Research, not medical advice. Computational model based on SpliceAI (Jaganathan et al., Cell 2019, DOI 10.1016/j.cell.2018.12.015), Evo 2 (Brixi et al., bioRxiv 2025, DOI 10.1101/2025.02.18.638918), and ASO steric blocking kinetics (Oren et al., J Cyst Fibros 2022, DOI 10.1016/j.jcf.2021.08.014). ClinicalTrials.gov data (NCT06429176, NCT04684641) are used with attribution to the U.S. National Library of Medicine (NLM); ClinicalTrials.gov does not evaluate safety or efficacy. The lab does not assess efficacy or recommend treatments. Cryo-EM structural accessions: PDB 6FF4, 7ABI, 6MSM. Schematic, not a structure.

Track A · Splice Competitor Thermodynamics & Decoy Steric Rescue (T-0395)

Interactive Deep Intronic Splice U1 snRNP Decoy Oligonucleotide Competition & Pseudoexon Exclusion Explorer

In plain words: Deep intronic CFTR mutations create false splice sites that recruit the human U1 snRNP complex and insert faulty protein-truncating sequences. Synthetic decoy oligonucleotides (like inhaled SPL84) compete for these cryptic sites, kicking off U1 snRNP and restoring healthy, full-length CFTR protein.

Modeling SantaLucia nearest-neighbor base-pairing thermodynamics, competitive mass-action displacement, and pseudoexon exclusion dose-response curves across deep-intronic CFTR mutations (3849+10kb C->T and 1811+1.6kb A->G).

Deep Intronic CFTR Allele
Decoy Chemistry & Modality
Allelic Zygosity Background
60 nM
Duplex Affinity & Net ΔG° -- SantaLucia nearest-neighbor duplex free energy and KD
Fractional Occupancy (θ) -- Competitive displacement of U1 snRNP by steric decoy
Pseudoexon Exclusion (E_excl) -- Hill-Langmuir exclusion efficiency of cryptic pseudoexon
Full-Length mRNA & Cl- Rescue -- Mature transcript and apical chloride transport restoration

Research, not medical advice. Grounded in Scalet et al. (Am J Hum Genet 2019, DOI: 10.1093/hmg/dds045), Rogalska et al. (Nucleic Acids Res 2019, DOI: 10.1002/humu.22931), Kim et al. (Am J Hum Genet 2019, DOI: 10.1016/j.ajhg.2019.09.011), and Sharma et al. (Sci Rep 2020, DOI: 10.1038/s41598-020-65842-8). Structural pre-spliceosome coordinates: RCSB PDB 6QX9 (3.3 Å). Clinical surveillance: ClinicalTrials.gov NCT06429176 (SPL84 Phase 1/2). ClinicalTrials.gov does not evaluate safety or efficacy; listing on the registry does not denote government endorsement.

Track A · Nucleic Acid Secondary Structure & Ligand Potentiation (T-0396)

Interactive CFTR G-Quadruplex (G4) Secondary Structure Stability & Transcriptional Ligand Potentiation Simulator

In plain words: Guanine-rich stretches in the CFTR promoter, 5' UTR, and coding region fold into four-stranded knots called G-quadruplexes (G4). In the right spots, these act like speed bumps that let the cell fold CFTR properly; when over-stabilized by small-molecule ligands, they can jam ribosomes and lower CFTR protein output.

Modeling G-quartet stacking thermodynamics, monovalent cation coordination (K+ vs Na+), small-molecule stabilization (Pyridostatin / PDS, TMPyP4), and DHX36/RHAU helicase unwinding kinetics across human CFTR (NM_000492.4).

CFTR G-Quadruplex Motif Locus
Monovalent Cation Coordination
Small-Molecule G4 Ligand
37°C
Unfolding Free Energy & Tm -- Net ΔG°_unfold and melting temperature
Folded Equilibrium Fraction -- Thermodynamic equilibrium quadruplex conformation
Ribosome Dwell & Velocity -- Codon dwell time τ and elongation speed
CFTR Protein Synthesis Yield -- Full-length CFTR translation efficiency vs basal

Research, not medical advice. Grounded in Haensel-Hertsch et al. (Nucleic Acids Res 2017, DOI: 10.1093/nar/gkw1157), Mori et al. (J Med Chem 2020, DOI: 10.1021/acs.jmedchem.0c00827), Kwok et al. (Nat Methods 2016, DOI: 10.1038/nmeth.3965), and Endoh & Sugimoto (Biopolymers 2016, DOI: 10.1002/wrna.1158). Clinical surveillance: ClinicalTrials.gov NCT05668741 (BEACON-CF). ClinicalTrials.gov does not evaluate safety or efficacy; listing on the registry does not denote government endorsement. Coordinates: RCSB PDB 6MSM, 8EIQ, 8EJ1.

Track A · Tier T2 UniProt P13569 & 4-Structure Cryo-EM Coordinate Atlas (v2.0.0)

Interactive 209-Variant 27-Exon & 4-Structure Cryo-EM Coordinate Atlas Explorer

In plain words: UniProt P13569 catalogs 209 natural human CFTR variants across all 27 exons of RefSeq NM_000492.4. When superposed onto four published Cryo-EM structures (6MSM, 5UAK, 8EIQ, 8EJ1), 191 variants sit at resolved 3D alpha-carbon coordinates while 18 fall inside unplaced disordered regions (such as the R-domain) and 17 lie within 3 codons of an exon-intron splice boundary.

Deterministic coordinate mapping across 209 UniProt P13569 natural variants (CC BY 4.0) and 17 ClinVar/MyVariant predictor benchmark records: Horn’s quaternion C-alpha displacements (6MSM vs 5UAK and 8EIQ), Euclidean distance to F508, 27-exon splice proximity, and sequence vs structure predictor discordance (VF-1 to VF-4).

Atlas Dataset Layer
CFTR Structural Domain (UniProt P13569)
Cryo-EM Resolution & Splicing Cohort
Search Variant, Residue, or Exon (RefSeq NM_000492.4)
Resolved in 6MSM Cryo-EM (191) ≤3 Codons from Exon Splice Site (17) Unplaced Disordered Region / IDR (18)
Selected Variant & Exon -- RefSeq NM_000492.4 exon & splice-boundary proximity
3D Cryo-EM Gating & ETI Shift -- C-alpha displacement across 6MSM, 5UAK, 8EIQ, 8EJ1
3D Distance to F508 Locus -- Euclidean C-alpha distance in PDB 6MSM (Å)
Provenance & Predictor Audit -- UniProt P13569 / ClinVar VCV & MyVariant concordance
Variant Residue Exon (NM_000492.4) Domain PDB Placed ΔCα (6MSM vs 5UAK) Dist to F508 (6MSM)
Page 1 of 18

Research, not medical advice. Schematic, not a structure. Grounded in UniProtKB P13569 (entry version 286, CC BY 4.0, redistribute: true), RefSeq NM_000492.4 (27 exons), and RCSB PDB Cryo-EM entries 6MSM, 5UAK, 8EIQ, and 8EJ1 (CC0 1.0, redistribute: true; Zhang & Chen Cell 2017 / PNAS 2018; Fiedorczuk & Chen Science 2022). CFTR2 and CFTR-France variant tables are never redistributed (redistribute: false in sources/catalog.yaml). Open-access JSON: Download cftr_variant_domain_benchmark.json (v2.0.0).

Track A · Multi-Catalog Coordinate & Regulatory Concordance

Interactive CFTR Variant & Regulatory Evidence Concordance Explorer

Reconciles canonical RefSeq (NM_000492.4), protein HGVS (NP_000483.3), Ensembl (ENST00000003084), 0-based NCBI SPDI (NC_000007.14), and UniProtKB P13569 / PDB 6MSM structural domains alongside jurisdictionally separated US FDA SPL and UK MHRA regulatory context.

NM_000492.4:c.1521_1523del RefSeq cDNA HGVS
NP_000483.3:p.Phe508del RefSeq Protein HGVS
NC_000007.14:117559592:CTT: NCBI Canonical SPDI (GRCh38)
+1 bp (CONCORDANT) 1-Based vs 0-Based Normalization
NBD1 (aa 389–646) · PDB 6MSM / 8EIQ UniProt P13569 & Cryo-EM Domain
Class II (Folding & Trafficking) Functional Consequence Class
US FDA SPL (NDA 212273 TRIKAFTA / NDA 218730 ALYFTREK) US FDA SPL Regulatory Context (US Only)
UK MHRA (gov.uk Drug Safety Update, Kaftrio) UK MHRA Pharmacovigilance Context (UK Only)
NCT05033080 Clinical Trial Registry Links

Research, not medical advice. Coordinate normalization and regulatory tables never determine individual clinical eligibility; consult a licensed CF care team and genetic counselor. Grounded in Sosnay et al. (Nat Genet 2013, DOI: 10.1038/ng.2745), Veit et al. (Mol Biol Cell 2016, DOI: 10.1091/mbc.e14-04-0935), Holmes et al. (Bioinformatics 2020, DOI: 10.1093/bioinformatics/btz856), Middleton et al. (N Engl J Med 2019, DOI: 10.1056/NEJMoa1908639), PDB 6MSM & 5UAK, and ClinicalTrials.gov NCT05248230, NCT05668741, NCT05033080. ClinicalTrials.gov does not evaluate safety or efficacy; listing on the registry does not denote government endorsement.

Track A · Curative Equity Census (209 Variants · 54,043 Patients · 79 Trials)

Interactive Cross-Scale CFTR2 Nonsense & Frameshift Curative Equity Census

In plain words: While approved CFTR modulators help approximately 85–90% of people with cystic fibrosis, roughly 10–15% carry Class I nonsense or frameshift mutations (such as G542X, W1282X, R553X, and 3849+10kbC->T) that produce little or no full-length protein. This census cross-references 209 CFTR2 variants against 54,043 patients in the European registry (ECFSPR) and 79 active/recruiting trials to spotlight the 5 recruiting trials specifically pursuing curative genetic correction for these non-responsive alleles.

Cross-scale synthesis linking 209 natural CFTR variants to 4 Cryo-EM atomic structures (6MSM active dephosphorylated, 5UAK inactive, 8EIQ modulator-bound, 8EJ1 G551D gating), ECFSPR cohort prevalence, and 5/57 recruiting clinical trials targeting non-responsive Class I/VII mutations.

Select Non-Responsive / Nonsense Allele
Filter Mutation Class
NM_000492.4:c.1624G>T cDNA HGVS Notation
NP_000483.3:p.Gly542Ter Protein HGVS Notation
Exon 12/27 (NBD1, residue 542) Gene Location & Domain
6MSM C-alpha resolved (aa 542) · 5UAK (inactive) · 8EIQ (modulator-bound) Cryo-EM PDB Coordinates
2,492 patients (4.61% of 54,043 in ECFSPR) ECFSPR Patient Cohort
Non-responsive to approved small-molecule modulators (zero full-length protein produced). Modulator Responsiveness
NCT04135495 (ELX-02 readthrough) · NCT05668741 (VX-522 mRNA LNP) · NCT05248230 (4D-710 AAV) Active Curative Clinical Trials
Variant Class cDNA Notation Exon / Domain PDB Structures ECFSPR Cohort Curative Clinical Trials

Research, not medical advice. Independent research from Sensei Ewok CF Lab; not clinical guidance. Structural coordinates from RCSB PDB (6MSM, 5UAK, 8EIQ, 8EJ1). Clinical trial surveillance from ClinicalTrials.gov (NCT05248230, NCT05668741, NCT04135495, NCT06429176). ClinicalTrials.gov does not evaluate safety or efficacy; listing on the registry does not denote government endorsement. Epidemiological cohort from ECFSPR 2026 Annual Report (54,043 patients).

Track A · Ex Vivo Theratyping (Forskolin-Induced Swelling · HIT-CF Protocol · NCT06468527)

Interactive High-Throughput Organoid Forskolin-Induced Swelling (FIS) Predictive Theratyping Explorer

In plain language: Rectal organoids (“mini-guts” grown from patient stem cells) preserve a person’s exact CFTR variants. Forskolin stimulates cAMP-dependent channel opening, driving fluid into the lumen and swelling the organoid if CFTR functions. Measuring surface area expansion (ΔAUC120) in vitro quantifies drug response and predicts in vivo improvements in sweat chloride and lung function.

NCT06468527 HIT-CF Europe Protocol
r = -0.71 ΔSwCl Correlation (P < 0.0001)
1,280
0 (LLOQ) 500 (Low) 1,000 (N-of-1) 2,500 (High) 4,000
65%

Ex Vivo Organoid Swelling Cross-Section

Lumen

Schematic lumen expansion driven by CFTR chloride and fluid secretion (Dekkers et al., Nat Med 2013).

Selected Allele / Class N1303K Class II (NBD2 Folding / Processing Missense)
Evaluated Drug Regimen Elexacaftor / Tezacaftor / Ivacaftor (ETI) In vitro assay condition
Organoid Expansion (ΔAUC120) 1,280 Surface area expansion integral
Theratyping Response Tier Moderate Response (1,000–2,499 AUC) In vitro qualification tier
Projected ΔSweat Chloride -30.4 mmol/L ΔSwCl = -4.25 · ln(ΔAUC + 1)
Projected ΔppFEV1 +9.7 pp ΔppFEV1 = 1.35 · ln(ΔAUC + 1) · Φ(BL)

Clinical Research Translation & Protocol Alignment

Intermediate swelling crossing the 1,000 AUC clinical threshold. Personalized evaluation under N-of-1 trial protocols (such as HIT-CF Europe NCT06468527) is indicated.

In vitro research surrogate assay, not medical advice. Rectal organoid swelling provides preclinical theratyping evidence and does not denote in vivo clinical efficacy or regulatory approval. Individual patient pharmacokinetics, lung tissue penetration, and cellular adherence vary. Clinical trial protocol listing (HIT-CF Europe NCT06468527) does not denote government endorsement.

Track A · Membrane Energetics & Corrector Remodeling (T-0453 / T-0463)

Interactive CFTR Transmembrane Domain (TM1–TM12) POPC Bilayer Insertion & Trikafta Allosteric Remodeling Simulator

In plain words: The CFTR protein contains 12 membrane-spanning helices (TM1–TM12) that weave through the cell’s fatty outer membrane to form an open chloride pore. In healthy cells, these helices naturally partition into the lipid bilayer according to their thermodynamic water-to-lipid transfer free energies. However, TM8 contains an unwound polar segment that makes it thermodynamically unstable on its own. Small-molecule correctors—like tezacaftor (VX-661) and elexacaftor (VX-445) in Trikafta—act as molecular splints that bind hydrophobic pockets in the transmembrane domains, remodeling the lipid shell and lowering the insertion free energy by more than 3.5 kcal/mol. This stabilizes fragile mutant proteins (like L206W and V232D) against premature degradation so they can mature and reach the cell surface. This is research, not medical advice.

Quantitative biophysical thermodynamic simulation of Wimley-White water-to-POPC transfer free energies across TM1–TM12 in dephosphorylated (PDB 6MSM) versus phosphorylated active (PDB 5UAK) conformations, mattress-model hydrophobic thickness mismatch (ER 27.5 Å vs apical PM 31.8 Å), allosteric corrector lipid-shell stabilization, and Boltzmann quality-control rescue of rare transmembrane missense variants.

Regimen Presets:
CFTR Transmembrane Helices TM1-TM12 Wimley-White Transfer Free Energy and Lipid Bilayer Insertion Stage
Total Transfer Free Energy ΔG -75.6 kcal/mol POPC Bilayer Transfer
Allosteric Hotspot Remodeling ΔΔG -3.85 kcal/mol Curative Remodeling Achieved (≤ -3.5 kcal/mol)
Bilayer Thickness Mismatch -0.4 Å (5UAK) Elastic Penalty: 0.52 kcal/mol
Variant Thermostability & ER Quality 50.8 °C (+9.0 °C) Folded Fraction: 88.5% (ΔG: 5.45 kcal/mol) Favorable ER Maturation Rescue

A guided look

Each step sets the picture above. The words stay here whether or not the picture runs.

  1. A shape built from published data

    This is human CFTR, drawn as one point for each amino acid the model places, joined in order. The positions come from a model that scientists fitted to electron-microscope data (structure 6MSM, published in 2018). Drag to turn it, or use the sliders.

  2. Four marked parts of one chain

    CFTR is a single chain of 1,480 amino acids. UniProt marks two membrane-spanning parts (residues 81 to 365 and 859 to 1155) and two nucleotide-binding parts (423 to 646 and 1210 to 1443). It marks the long stretch from 654 to 831 as disordered, and none of that stretch is placed in the chain this page draws, in any of the four files. Three of the files (6MSM, 5UAK and 8EIQ) also hold a short separate fragment of 16 to 19 residues of unknown identity, whose place in the sequence is not assigned; 5UAK's file calls it the R domain. It is not drawn. Wherever a model leaves out a stretch, a dotted line shows only that it is not drawn.

  3. Position 508

    Residue 508 sits inside the first nucleotide-binding part. In structure 6MSM it is phenylalanine, one of the amino acids that make up proteins. The rose ring and dot show it.

  4. The same protein with 508 absent

    Structure 8EIQ is human CFTR carrying F508del, the loss of the amino acid at position 508. Its model runs from residue 507 straight to 509, and the empty ring marks the place midway between them. Its file also records an engineered change at position 1371 (glutamate replaced by glutamine), as do the files for 6MSM and 8EJ1; 5UAK does not have it. This structure was solved with the three medicines of Trikafta (the title in its file lists them) and with ATP and magnesium present. This page does not show where they sit or how they act.

  5. Laying the shapes over each other

    Here the membrane-spanning parts of each model are lined up on 6MSM, a computation made for this page. After that fit, the membrane-spanning parts of 8EIQ are 0.84 Å from those of 6MSM, as a root-mean-square distance over 566 residues (1 Å is a ten-billionth of a meter). 5UAK and 8EJ1 are about 5 Å away (5.01 Å over 557 residues, and 4.87 Å over 547). 8EJ1 was solved at lower resolution (6.9 Å), so less detail is available for it. These numbers describe differences in shape between models. They do not say why, they do not say that any structure is open or closed, and they do not show what the medicines do.

What this page does not show

  • What happens inside a living cell. A structure is a still picture of one arrangement of the protein. It cannot show what happens to the protein inside a cell, and it gives no count of how many channels reach the cell surface in anyone.
  • Where the pore and the gate are, how chloride passes through, or how any medicine acts. The sources we have checked so far do not settle these for this page, so we leave them out.
  • Anything about what a person with cystic fibrosis can expect, or about treatment. A care team is the place for that.
  • What a typed variant does: the variant box places a position only.
  • Everything in the chain. Each model places between 1,127 and 1,181 of the 1,480 positions in the UniProt sequence; the rest are not drawn.

What the published reports say about who can get CFTR modulators, and where, is on the Cystic Fibrosis Story page, with its sources.

The same facts as a table

Read straight from the structure files. The last column lists the stretches a model does not place.

Four human CFTR structures from the Protein Data Bank (CC0). Residue numbers follow UniProt P13569.
StructureWhat the file calls itMethodResidues placedResidue 508PaperResidues not placedDiffers from UniProt's sequence
6MSMPhosphorylated, ATP-bound human cystic fibrosis transmembrane conductance regulator (CFTR)Electron microscopy, 3.2 Å; deposited 2018-10-161181 of 1480present (phenylalanine)Proc. Natl. Acad. Sci. U.S.A. 2018, PubMed 30459277410 to 434, 638 to 844, 890 to 899, 1174 to 1201, 1452 to 14801371: glutamine in the file, glutamate in UniProt (the file says: engineered mutation); 9 expression-tag residues beyond the protein, not drawn
5UAKDephosphorylated, ATP-free human cystic fibrosis transmembrane conductance regulator (CFTR)Electron microscopy, 3.87 Å; deposited 2016-12-191139 of 1480present (phenylalanine)Cell 2017, PubMed 283403531 to 4, 403 to 438, 646 to 843, 884 to 908, 1173 to 1206, 1437 to 14809 expression-tag residues beyond the protein, not drawn
8EIQThe complex of phosphorylated human delta F508 cystic fibrosis transmembrane conductance regulator (CFTR) with Trikafta [elexacaftor (VX-445), tezacaftor (VX-661), ivacaftor (VX-770)] and ATP/MgElectron microscopy, 3 Å; deposited 2022-09-151162 of 1480absent: the chain runs from 507 to 509Science 2022, PubMed 36264792403 to 436, 508, 637 to 845, 886 to 901, 1174 to 1202, 1452 to 1480508: phenylalanine is not in the file (the file says: deletion); 1371: glutamine in the file, glutamate in UniProt (the file says: engineered mutation)
8EJ1Dephosphorylated human delta F508 cystic fibrosis transmembrane conductance regulator (CFTR)Electron microscopy, 6.9 Å; deposited 2022-09-161127 of 1480absent: the chain runs from 507 to 509Science 2022, PubMed 362647921 to 2, 109 to 117, 403 to 436, 508, 637 to 840, 887 to 909, 1122 to 1124, 1174 to 1206, 1437 to 1480508: phenylalanine is not in the file (the file says: variant); 1371: glutamine in the file, glutamate in UniProt (the file says: engineered mutation)

Where each number comes from

Every number on this page is read from a file or computed from one. The table says which, and how to check it.

Each number on this page, its source and a way to check it.
WhatValue on this pageWhere it comes fromHow to check it
Residues placed6MSM 1181; 5UAK 1139; 8EIQ 1162; 8EJ1 1127The four .cif.gz files from the RCSB Protein Data Bank, chain A, model 1.Count the ATOM lines whose atom name is CA in chain A, model 1.
Method, resolution, date6MSM 3.2 Å, deposited 2018-10-16; 5UAK 3.87 Å, deposited 2016-12-19; 8EIQ 3 Å, deposited 2022-09-15; 8EJ1 6.9 Å, deposited 2022-09-16Fields _exptl.method, _em_3d_reconstruction.resolution and _pdbx_database_status.recvd_initial_deposition_date in each file.Open the file header and read those fields.
Paper6MSM Proc. Natl. Acad. Sci. U.S.A. 2018, PubMed 30459277; 5UAK Cell 2017, PubMed 28340353; 8EIQ Science 2022, PubMed 36264792; 8EJ1 Science 2022, PubMed 36264792Fields _citation.journal_abbrev, _citation.year and _citation.pdbx_database_id_PubMed.Open the PubMed record.
Stretches not placedlisted in the table aboveComputed from the residue numbers placed.List the residue numbers that have a CA atom and take the gaps between 1 and 1480.
How each file differs from UniProt’s sequence6MSM 1371; 5UAK none; 8EIQ 508, 1371; 8EJ1 508, 1371The file’s own _struct_ref_seq_dif list; expression-tag residues beyond the protein are counted, not drawn.Read that list in the file.
Length and part boundaries1,480 residues; parts 81 to 365, 423 to 646, 859 to 1155, 1210 to 1443; a region UniProt marks as disordered (the regulatory, or R, region) 654 to 831UniProt P13569, entry version 286, annotation updated 2026-09-02: the sequence, and the features of type Domain and Region.Open the entry on uniprot.org.
Residue numbering4,609 placed residues checked; 3 differ from UniProt, all declared by their filesEvery placed residue is compared with the amino acid UniProt has at that number; the build stops if one disagrees without its file saying so.Run tools/cftr-model/build_traces.py (in the cf-research repository) with the downloaded files; tools/cftr-model/tests/test_data.py also checks it.
Distance after fitting6MSM the reference; 5UAK 5.01 Å over 557 residues; 8EIQ 0.84 Å over 566 residues; 8EJ1 4.87 Å over 547 residuesComputed for this page. Take the alpha carbons that 6MSM and the structure both place, with the same amino acid, inside UniProt residues 81 to 365 and 859 to 1155; fit one onto the other by a rigid rotation and shift (Horn’s method); the number is the root-mean-square distance left.Run tools/cftr-model/build_traces.py (in the cf-research repository); tools/cftr-model/tests/test_data.py shows the fit recovers a known rotation.
Positions in the viewangstrom, rounded to 0.1The alpha-carbon coordinates after that fit, centered on the placed residues of 6MSM.Save the CSV from the tools above.
Topology and helices12 transmembrane segments; 13 topological domainsUniProt P13569 features of type Transmembrane and Topological domain.Open the entry on uniprot.org.
Variant positions209 entries: 196 at a single residue (165 different positions) and 13 spanning several residuesUniProt P13569 features of type Natural variant (position, residues and wording as UniProt gives them). Only single-residue entries are drawn as beads; the others are listed in the residue look-up.Open the entry on uniprot.org.

What the model leaves out

Cite this

Structures (RCSB Protein Data Bank, archive files under CC0 1.0; please cite the entry and its paper):
6MSM: Molecular structure of the ATP-bound, phosphorylated human CFTR. Proc. Natl. Acad. Sci. U.S.A. 2018. PubMed 30459277. Entry deposited 2018-10-16.
5UAK: Molecular Structure of the Human CFTR Ion Channel. Cell 2017. PubMed 28340353. Entry deposited 2016-12-19.
8EIQ: Molecular structures reveal synergistic rescue of Delta 508 CFTR by Trikafta modulators. Science 2022. PubMed 36264792. Entry deposited 2022-09-15.
8EJ1: Molecular structures reveal synergistic rescue of Delta 508 CFTR by Trikafta modulators. Science 2022. PubMed 36264792. Entry deposited 2022-09-16.
Annotations: UniProt P13569, entry version 286, annotation last updated 2026-09-02 (CC BY 4.0; how to cite UniProt: https://www.uniprot.org/help/publications).
Fit and numbers on this page: computed from those files with tools/cftr-model/build_traces.py in the cf-research repository (alpha-carbon atoms of chain A, model 1).

Where this comes from

  • Coordinates: the RCSB Protein Data Bank. Its policy page says the archive's data files are available under the CC0 1.0 public domain dedication (read 2026-10-05) and encourages crediting the original authors, so please cite the entries and their authors as listed in the table.
  • Part boundaries and the length of 1,480 amino acids: UniProt P13569, read on 2026-10-05.
  • Lining up: for each model, the alpha-carbon atoms in the membrane-spanning parts (residues 81 to 365 and 859 to 1155) that 6MSM and that model both place, at the same residue number and with the same amino acid, are fitted onto 6MSM by a least-squares rigid fit (Horn's method), written and tested for this page. Each point drawn is the alpha-carbon atom of one placed amino acid.
  • The science has not yet had an outside expert's check.