8ETP

Cryo-EM structure of cGMP bound closed state of human CNGA3/CNGB3 channel in GDN


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Conformational trajectory of allosteric gating of the human cone photoreceptor cyclic nucleotide-gated channel.

Hu, Z.Zheng, X.Yang, J.

(2023) Nat Commun 14: 4284-4284

  • DOI: https://doi.org/10.1038/s41467-023-39971-8
  • Primary Citation of Related Structures:  
    8ETP, 8EU3, 8EUC, 8EV8, 8EV9, 8EVA, 8EVB, 8EVC

  • PubMed Abstract: 

    Cyclic nucleotide-gated (CNG) channels transduce chemical signals into electrical signals in sensory receptors and neurons. They are activated by cGMP or cAMP, which bind to the cyclic nucleotide-binding domain (CNBD) to open a gate located 50-60 Å away in the central cavity. Structures of closed and open vertebrate CNG channels have been solved, but the conformational landscape of this allosteric gating remains to be elucidated and enriched. Here, we report structures of the cGMP-activated human cone photoreceptor CNGA3/CNGB3 channel in closed, intermediate, pre-open and open states in detergent or lipid nanodisc, all with fully bound cGMP. The pre-open and open states are obtained only in the lipid nanodisc, suggesting a critical role of lipids in tuning the energetic landscape of CNGA3/CNGB3 activation. The different states exhibit subunit-unique, incremental and distinct conformational rearrangements that originate in the CNBD, propagate through the gating ring to the transmembrane domain, and gradually open the S6 cavity gate. Our work illustrates a spatial conformational-change wave of allosteric gating of a vertebrate CNG channel by its natural ligand and provides an expanded framework for studying CNG properties and channelopathy.


  • Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic nucleotide-gated cation channel alpha-3
A, B, C
694Homo sapiensMutation(s): 0 
Gene Names: CNGA3CNCG3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16281 (Homo sapiens)
Explore Q16281 
Go to UniProtKB:  Q16281
PHAROS:  Q16281
GTEx:  ENSG00000144191 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16281
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q16281-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic nucleotide-gated cation channel beta-3809Homo sapiensMutation(s): 0 
Gene Names: CNGB3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQW8 (Homo sapiens)
Explore Q9NQW8 
Go to UniProtKB:  Q9NQW8
PHAROS:  Q9NQW8
GTEx:  ENSG00000170289 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NQW8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCG (Subject of Investigation/LOI)
Query on PCG

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
K [auth D]
CYCLIC GUANOSINE MONOPHOSPHATE
C10 H12 N5 O7 P
ZOOGRGPOEVQQDX-UUOKFMHZSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-02
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary