9Y1Q | pdb_00009y1q

Alternative NBD1-binding geometry in channel-formed, ATP-bound, VX809-bound, T2a-nanobody-bound wild-type human CFTR (Composite map from PHENIX)

PDB DOI: https://doi.org/10.2210/pdb9Y1Q/pdb
EM Map EMD-72403: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Lama glama
Expression System: Cricetulus griseus, Escherichia coli
Mutation(s): Yes

Deposited: 2025-08-30 Released: 2026-09-09
Deposition Author(s): Hunt, J.F., Paige, A.S., Govaerts, C.
Funding Organization(s): Cystic Fibrosis Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.86 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Nanobody-Driven Stabilization Synergistically Rescues F508del-CFTR and Reveals an Alternative Active State of the Channel

Hunt, F.J., Paige, A.S., Cohen, B.M., Goldberg, P.M., Wang, C., Loughlin, B.J., Kappes, J.C., Yang, Z., Jiang, F., Govaerts, C., Overtus, M., Urbatsch, I.L., Lukacs, G.

To be published.

Macromolecule Content

Total Structure Weight: 203.34 kDa
Atom Count: 10,083
Modeled Residue Count: 1,179
Deposited Residue Count: 1,686
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystic fibrosis transmembrane conductance regulator	A	1,523	Homo sapiens	Mutation(s): 1 Gene Names: CFTR, ABCC7 EC: 5.6.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for P13569 (Homo sapiens) Explore P13569 Go to UniProtKB: P13569
PHAROS: P13569 GTEx: ENSG00000001626
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13569
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T2a nanobody	B	146	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK	C	17	Homo sapiens	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 15 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AJP Query on AJP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	Digitonin C₅₆ H₉₂ O₂₉ UVYVLBIGDKGWPX-KUAJCENISA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
P5S Query on P5S Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine C₄₂ H₈₂ N O₁₀ P TZCPCKNHXULUIY-RGULYWFUSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
PC1 Query on PC1 Download:Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain J [auth A] MOL2 format, chain U [auth A] MOL2 format, chain J [auth A] mmCIF format, chain U [auth A] mmCIF format, chain J [auth A]	J [auth A], U [auth A]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain J [auth A] Focus chain U [auth A] Interactions & Density Focus chain J [auth A] Focus chain U [auth A]
PTY Query on PTY Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain L [auth A] MOL2 format, chain T [auth A] MOL2 format, chain L [auth A] mmCIF format, chain T [auth A] mmCIF format, chain L [auth A]	L [auth A], T [auth A]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain L [auth A] Focus chain T [auth A] Interactions & Density Focus chain L [auth A] Focus chain T [auth A]
3PH Query on 3PH Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain K [auth A] SDF format, chain AA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain K [auth A] mmCIF format, chain AA [auth A]	AA [auth A], K [auth A], Z [auth A]	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE C₃₉ H₇₇ O₈ P YFWHNAWEOZTIPI-DIPNUNPCSA-N		Interactions Focus chain AA [auth A] Focus chain K [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain K [auth A] Focus chain Z [auth A]
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain GA [auth A] SDF format, chain EA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain EA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain EA [auth A]	EA [auth A], GA [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain EA [auth A] Focus chain GA [auth A] Interactions & Density Focus chain EA [auth A] Focus chain GA [auth A]
VX8 Query on VX8 Download:Ideal Coordinates CCD File SDF format, chain IA [auth A] MOL2 format, chain IA [auth A] mmCIF format, chain IA [auth A]	IA [auth A]	Lumacaftor C₂₄ H₁₈ F₂ N₂ O₅ UFSKUSARDNFIRC-UHFFFAOYSA-N		Interactions Focus chain IA [auth A] Interactions & Density Focus chain IA [auth A]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain X [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain X [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], X [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain X [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain X [auth A]
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	M [auth A], N [auth A], O [auth A], Y [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Y [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Y [auth A]
MYR Query on MYR Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
D12 Query on D12 Download:Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain Q [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain Q [auth A]	Q [auth A], V [auth A], W [auth A]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain Q [auth A] Focus chain V [auth A] Focus chain W [auth A]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]
OCT Query on OCT Download:Ideal Coordinates CCD File SDF format, chain CA [auth A] MOL2 format, chain CA [auth A] mmCIF format, chain CA [auth A]	CA [auth A]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Interactions & Density Focus chain CA [auth A]
HEX Query on HEX Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain DA [auth A] SDF format, chain BA [auth A] MOL2 format, chain S [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain BA [auth A] mmCIF format, chain S [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain BA [auth A]	BA [auth A], DA [auth A], S [auth A]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain DA [auth A] Focus chain S [auth A] Interactions & Density Focus chain BA [auth A] Focus chain DA [auth A] Focus chain S [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain HA [auth A] SDF format, chain FA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain FA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain FA [auth A]	FA [auth A], HA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain FA [auth A] Focus chain HA [auth A] Interactions & Density Focus chain FA [auth A] Focus chain HA [auth A]