6L3U

Human Cx31.3/GJC3 connexin hemichannel in the presence of calcium


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 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

Cryo-EM structure of human Cx31.3/GJC3 connexin hemichannel.

Lee, H.J.Jeong, H.Hyun, J.Ryu, B.Park, K.Lim, H.H.Yoo, J.Woo, J.S.

(2020) Sci Adv 6: eaba4996-eaba4996

  • DOI: https://doi.org/10.1126/sciadv.aba4996
  • Primary Citation of Related Structures:  
    6L3T, 6L3U, 6L3V

  • PubMed Abstract: 

    Connexin family proteins assemble into hexameric channels called hemichannels/connexons, which function as transmembrane channels or dock together to form gap junction intercellular channels (GJIChs). We determined the cryo-electron microscopy structures of human connexin 31.3 (Cx31.3)/GJC3 hemichannels in the presence and absence of calcium ions and with a hearing-loss mutation R15G at 2.3-, 2.5-, and 2.6-Å resolutions, respectively. Compared with available structures of GJICh in open conformation, Cx31.3 hemichannel shows substantial structural changes of highly conserved regions in the connexin family, including opening of calcium ion-binding tunnels, reorganization of salt-bridge networks, exposure of lipid-binding sites, and collocation of amino-terminal helices at the cytoplasmic entrance. We also found that the hemichannel has a pore with a diameter of ~8 Å and selectively transports chloride ions. Our study provides structural insights into the permeant selectivity of Cx31.3 hemichannel.


  • Organizational Affiliation

    Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gap junction gamma-3 protein
A, B, C, D, E
A, B, C, D, E, F
279Homo sapiensMutation(s): 0 
Gene Names: GJC3GJE1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFK1 (Homo sapiens)
Explore Q8NFK1 
Go to UniProtKB:  Q8NFK1
PHAROS:  Q8NFK1
GTEx:  ENSG00000176402 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NFK1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMN (Subject of Investigation/LOI)
Query on LMN

Download Ideal Coordinates CCD File 
G [auth A]
I [auth A]
J [auth B]
L [auth C]
N [auth D]
G [auth A],
I [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E]
Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-XYPZXBMFSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
H [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
H [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
R [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.14

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2018R1C1B6004447

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 1.2: 2020-10-14
    Changes: Database references
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Structure summary