7BYM

Cryo-EM structure of human KCNQ4 with retigabine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Basis for the Modulation of Human KCNQ4 by Small-Molecule Drugs.

Li, T.Wu, K.Yue, Z.Wang, Y.Zhang, F.Shen, H.

(2021) Mol Cell 81: 25

  • DOI: https://doi.org/10.1016/j.molcel.2020.10.037
  • Primary Citation of Related Structures:  
    7BYL, 7BYM, 7BYN

  • PubMed Abstract: 

    Among the five KCNQ channels, also known as the K v 7 voltage-gated potassium (K v ) channels, KCNQ2-KCNQ5 control neuronal excitability. Dysfunctions of KCNQ2-KCNQ5 are associated with neurological disorders such as epilepsy, deafness, and neuropathic pain. Here, we report the cryoelectron microscopy (cryo-EM) structures of human KCNQ4 and its complexes with the opener retigabine or the blocker linopirdine at overall resolutions of 2.5, 3.1, and 3.3 Å, respectively. In all structures, a phosphatidylinositol 4,5-bisphosphate (PIP 2 ) molecule inserts its head group into a cavity within each voltage-sensing domain (VSD), revealing an unobserved binding mode for PIP 2 . Retigabine nestles in each fenestration, inducing local shifts. Instead of staying within the central pore, linopirdine resides in a cytosolic cavity underneath the inner gate. Electrophysiological analyses of various mutants corroborated the structural observations. Our studies reveal the molecular basis for the modulatory mechanism of neuronal KCNQ channels and provide a framework for structure-facilitated drug discovery targeting these important channels.


  • Organizational Affiliation

    Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein,Potassium voltage-gated channel subfamily KQT member 4A,
B [auth C],
C [auth E],
D [auth G]
979Aequorea victoriaHomo sapiens
This entity is chimeric
Mutation(s): 5 
Gene Names: GFPKCNQ4
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Find proteins for P56696 (Homo sapiens)
Explore P56696 
Go to UniProtKB:  P56696
PHAROS:  P56696
GTEx:  ENSG00000117013 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP42212P56696
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-3E [auth B],
F [auth D],
G [auth F],
H
149Homo sapiensMutation(s): 0 
Gene Names: CALM3CALML2CAM3CAMCCAMIII
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP25 (Homo sapiens)
Explore P0DP25 
Go to UniProtKB:  P0DP25
PHAROS:  P0DP25
GTEx:  ENSG00000160014 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP25
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PT5 (Subject of Investigation/LOI)
Query on PT5

Download Ideal Coordinates CCD File 
I [auth A],
O [auth C],
Q [auth E],
S [auth G]
[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate
C47 H85 O19 P3
CNWINRVXAYPOMW-HJBQCNPJSA-N
FBX (Subject of Investigation/LOI)
Query on FBX

Download Ideal Coordinates CCD File 
J [auth A],
N [auth C],
P [auth E],
R [auth G]
ethyl N-[2-azanyl-4-[(4-fluorophenyl)methylamino]phenyl]carbamate
C16 H18 F N3 O2
PCOBBVZJEWWZFR-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
M [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FBX BindingDB:  7BYM EC50: min: 1980, max: 5900 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references
  • Version 1.2: 2021-01-27
    Changes: Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references