7F8J

Cryo-EM structure of human pannexin-1 in a nanodisc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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 in nanodiscs reveal gating mediated by dynamic movement of the N terminus and phospholipids.

Kuzuya, M.Hirano, H.Hayashida, K.Watanabe, M.Kobayashi, K.Terada, T.Mahmood, M.I.Tama, F.Tani, K.Fujiyoshi, Y.Oshima, A.

(2022) Sci Signal 15: eabg6941-eabg6941

  • DOI: https://doi.org/10.1126/scisignal.abg6941
  • Primary Citation of Related Structures:  
    7F8J, 7F8N, 7F8O, 7WSV

  • PubMed Abstract: 

    Pannexin (PANX) family proteins form large-pore channels that mediate purinergic signaling. We analyzed the cryo-EM structures of human PANX1 in lipid nanodiscs to elucidate the gating mechanism and its regulation by the amino terminus in phospholipids. The wild-type channel has an amino-terminal funnel in the pore, but in the presence of the inhibitor probenecid, a cytoplasmically oriented amino terminus and phospholipids obstruct the pore. Functional analysis using whole-cell patch-clamp and oocyte voltage clamp showed that PANX1 lacking the amino terminus did not open and had a dominant negative effect on channel activity, thus confirming that the amino-terminal domain played an essential role in channel opening. These observations suggest that dynamic conformational changes in the amino terminus of human PANX1 are associated with lipid movement in and out of the pore. Moreover, the data provide insight into the gating mechanism of PANX1 and, more broadly, other large-pore channels.


  • Organizational Affiliation

    Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.


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
426Homo 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
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LBN
Query on LBN

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
EA [auth D]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth E],
GA [auth E],
H [auth A],
HA [auth E],
I [auth A],
IA [auth E],
J [auth A],
JA [auth E],
K [auth A],
KA [auth E],
L [auth A],
LA [auth F],
M [auth A],
MA [auth F],
N [auth B],
NA [auth F],
O [auth B],
OA [auth F],
P [auth B],
PA [auth F],
Q [auth B],
QA [auth F],
R [auth B],
RA [auth G],
S [auth B],
SA [auth G],
T [auth C],
TA [auth G],
U [auth C],
UA [auth G],
V [auth C],
VA [auth G],
W [auth C],
WA [auth G],
X [auth C],
Y [auth C],
Z [auth D]
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
C42 H82 N O8 P
WTJKGGKOPKCXLL-VYOBOKEXSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-26
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Source and taxonomy
  • Version 1.2: 2022-02-23
    Changes: Database references
  • Version 1.3: 2024-11-13
    Changes: Data collection, Structure summary