6WBN

Cryo-EM structure of human Pannexin 1 channel N255A mutant, gap junction

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): Yes 
  • Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc

  • 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: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 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, H, I, J, K, L, M, N
373Homo sapiensMutation(s): 1 
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
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
BB [auth G]
DA [auth C]
EC [auth L]
GB [auth H]
JA [auth D]
BB [auth G],
DA [auth C],
EC [auth L],
GB [auth H],
JA [auth D],
KC [auth M],
MB [auth I],
PA [auth E],
Q [auth A],
RC [auth N],
SB [auth J],
VA [auth F],
X [auth B],
YB [auth K]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
PTY
Query on PTY

Download Ideal Coordinates CCD File 
AB [auth G]
BA [auth C]
CA [auth C]
CC [auth L]
DC [auth L]
AB [auth G],
BA [auth C],
CA [auth C],
CC [auth L],
DC [auth L],
EB [auth H],
FB [auth H],
HA [auth D],
IA [auth D],
IC [auth M],
JC [auth M],
KB [auth I],
LB [auth I],
NA [auth E],
O [auth A],
OA [auth E],
P [auth A],
PC [auth N],
QB [auth J],
QC [auth N],
RB [auth J],
TA [auth F],
UA [auth F],
V [auth B],
W [auth B],
WB [auth K],
XB [auth K],
ZA [auth G]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
DGA
Query on DGA

Download Ideal Coordinates CCD File 
AA [auth B]
BC [auth K]
GA [auth C]
HC [auth L]
JB [auth H]
AA [auth B],
BC [auth K],
GA [auth C],
HC [auth L],
JB [auth H],
MA [auth D],
NC [auth M],
OC [auth N],
PB [auth I],
R [auth A],
SA [auth E],
U [auth A],
VB [auth J],
YA [auth F]
DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
AC [auth K]
CB [auth G]
DB [auth G]
EA [auth C]
FA [auth C]
AC [auth K],
CB [auth G],
DB [auth G],
EA [auth C],
FA [auth C],
FC [auth L],
GC [auth L],
HB [auth H],
IB [auth H],
KA [auth D],
LA [auth D],
LC [auth M],
MC [auth M],
NB [auth I],
OB [auth I],
QA [auth E],
RA [auth E],
S [auth A],
SC [auth N],
T [auth A],
TB [auth J],
TC [auth N],
UB [auth J],
WA [auth F],
XA [auth F],
Y [auth B],
Z [auth B],
ZB [auth K]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 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 2.0: 2021-06-30
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-10-16
    Changes: Data collection, Database references, Structure summary