6WBL

Cryo-EM structure of human Pannexin 1 channel with deletion of N-terminal helix and C-terminal tail, in complex with CBX

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 
  • Membrane Protein: Yes  OPMPDBTMmpstruc

  • Deposited: 2020-03-26 Released: 2020-06-03 
  • Deposition Author(s): Lu, W., Du, J., Ruan, Z.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), American Heart Association

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.13 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

Structures of human pannexin 1 reveal ion pathways and mechanism of gating.

Ruan, Z.Orozco, I.J.Du, J.Lu, W.

(2020) Nature 584: 646-651

  • DOI: https://doi.org/10.1038/s41586-020-2357-y
  • Primary Citation of Related Structures:  
    6WBF, 6WBG, 6WBI, 6WBK, 6WBL, 6WBM, 6WBN

  • PubMed Abstract: 

    Pannexin 1 (PANX1) is an ATP-permeable channel with critical roles in a variety of physiological functions such as blood pressure regulation 1 , apoptotic cell clearance 2 and human oocyte development 3 . Here we present several structures of human PANX1 in a heptameric assembly at resolutions of up to 2.8 angström, including an apo state, a caspase-7-cleaved state and a carbenoxolone-bound state. We reveal a gating mechanism that involves two ion-conducting pathways. Under normal cellular conditions, the intracellular entry of the wide main pore is physically plugged by the C-terminal tail. Small anions are conducted through narrow tunnels in the intracellular domain. These tunnels connect to the main pore and are gated by a long linker between the N-terminal helix and the first transmembrane helix. During apoptosis, the C-terminal tail is cleaved by caspase, allowing the release of ATP through the main pore. We identified a carbenoxolone-binding site embraced by W74 in the extracellular entrance and a role for carbenoxolone as a channel blocker. We identified a gap-junction-like structure using a glycosylation-deficient mutant, N255A. Our studies provide a solid foundation for understanding the molecular mechanisms underlying the channel gating and inhibition of PANX1 and related large-pore channels.


  • Organizational Affiliation

    Van Andel Institute, Grand Rapids, MI, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pannexin-1
A, B, C, D, E
A, B, C, D, E, F, G
370Homo sapiensMutation(s): 0 
Gene Names: PANX1MRS1UNQ2529/PRO6028
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RD7 (Homo sapiens)
Explore Q96RD7 
Go to UniProtKB:  Q96RD7
PHAROS:  Q96RD7
GTEx:  ENSG00000110218 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RD7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
CBO BindingDB:  6WBL IC50: 1.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.1b

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR56HL144929
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS111031
American Heart AssociationUnited States20POST35120556

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: 2020-09-09
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references