6WEJ

Structure of cGMP-unbound WT TAX-4 reconstituted in lipid nanodiscs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanism of ligand activation of a eukaryotic cyclic nucleotide-gated channel.

Zheng, X.Fu, Z.Su, D.Zhang, Y.Li, M.Pan, Y.Li, H.Li, S.Grassucci, R.A.Ren, Z.Hu, Z.Li, X.Zhou, M.Li, G.Frank, J.Yang, J.

(2020) Nat Struct Mol Biol 27: 625-634

  • DOI: https://doi.org/10.1038/s41594-020-0433-5
  • Primary Citation of Related Structures:  
    6WEJ, 6WEK, 6WEL

  • PubMed Abstract: 

    Cyclic nucleotide-gated (CNG) channels convert cyclic nucleotide (CN) binding and unbinding into electrical signals in sensory receptors and neurons. The molecular conformational changes underpinning ligand activation are largely undefined. We report both closed- and open-state atomic cryo-EM structures of a full-length Caenorhabditis elegans cyclic GMP-activated channel TAX-4, reconstituted in lipid nanodiscs. These structures, together with computational and functional analyses and a mutant channel structure, reveal a double-barrier hydrophobic gate formed by two S6 amino acids in the central cavity. cGMP binding produces global conformational changes that open the cavity gate located ~52 Å away but do not alter the structure of the selectivity filter-the commonly presumed activation gate. Our work provides mechanistic insights into the allosteric gating and regulation of CN-gated and nucleotide-modulated channels and CNG channel-related channelopathies.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic nucleotide-gated cation channel
A, B, C, D
733Caenorhabditis elegansMutation(s): 0 
Gene Names: tax-4ZC84.2
Membrane Entity: Yes 
UniProt
Find proteins for Q03611 (Caenorhabditis elegans)
Explore Q03611 
Go to UniProtKB:  Q03611
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03611
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CPL
Query on CPL

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
DA [auth D]
E [auth A]
EA [auth D]
AA [auth C],
BA [auth C],
DA [auth D],
E [auth A],
EA [auth D],
F [auth A],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
N [auth B],
O [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
V [auth C],
W [auth C],
Y [auth C],
Z [auth C]
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C42 H80 N O8 P
JLPULHDHAOZNQI-ZTIMHPMXSA-N
PX2 (Subject of Investigation/LOI)
Query on PX2

Download Ideal Coordinates CCD File 
CA [auth C]
FA [auth D]
G [auth A]
KA [auth D]
L [auth A]
CA [auth C],
FA [auth D],
G [auth A],
KA [auth D],
L [auth A],
P [auth B],
U [auth B],
X [auth C]
1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
C27 H52 O8 P
OKLASJZQBDJAPH-RUZDIDTESA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
M [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

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 StatesRO1EY027800
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM085234
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM055440
National Natural Science Foundation of China (NSFC)China21625302
National Natural Science Foundation of China (NSFC)China21573217
National Natural Science Foundation of China (NSFC)China31700647

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-06-17
    Changes: Database references
  • Version 1.2: 2020-07-22
    Changes: Database references