6UZY

Cryo-EM structure of Xenopus tropicalis pannexin 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structures of the ATP release channel pannexin 1.

Deng, Z.He, Z.Maksaev, G.Bitter, R.M.Rau, M.Fitzpatrick, J.A.J.Yuan, P.

(2020) Nat Struct Mol Biol 27: 373-381

  • DOI: https://doi.org/10.1038/s41594-020-0401-0
  • Primary Citation of Related Structures:  
    6UZY, 6V6D

  • PubMed Abstract: 

    The plasma membrane adenosine triphosphate (ATP) release channel pannexin 1 (PANX1) has been implicated in many physiological and pathophysiological processes associated with purinergic signaling, including cancer progression, apoptotic cell clearance, inflammation, blood pressure regulation, oocyte development, epilepsy and neuropathic pain. Here we present near-atomic-resolution structures of human and frog PANX1 determined by cryo-electron microscopy that revealed a heptameric channel architecture. Compatible with ATP permeation, the transmembrane pore and cytoplasmic vestibule were exceptionally wide. An extracellular tryptophan ring located at the outer pore created a constriction site, potentially functioning as a molecular sieve that restricts the size of permeable substrates. The amino and carboxyl termini, not resolved in the density map, appeared to be structurally dynamic and might contribute to narrowing of the pore during channel gating. In combination with functional characterization, this work elucidates the previously unknown architecture of pannexin channels and establishes a foundation for understanding their unique channel properties.


  • Organizational Affiliation

    Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pannexin
A, B, C, D, E
A, B, C, D, E, F, G
437Xenopus tropicalisMutation(s): 0 
Gene Names: panx1LOC100170473PANX
Membrane Entity: Yes 
UniProt
Find proteins for B3DLA5 (Xenopus tropicalis)
Explore B3DLA5 
Go to UniProtKB:  B3DLA5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3DLA5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6OU (Subject of Investigation/LOI)
Query on 6OU

Download Ideal Coordinates CCD File 
AA [auth G]
H [auth A]
K [auth B]
N [auth C]
Q [auth D]
AA [auth G],
H [auth A],
K [auth B],
N [auth C],
Q [auth D],
T [auth E],
W [auth F]
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
C39 H76 N O8 P
FHQVHHIBKUMWTI-OTMQOFQLSA-N
R16 (Subject of Investigation/LOI)
Query on R16

Download Ideal Coordinates CCD File 
BA [auth G]
I [auth A]
J [auth A]
L [auth B]
M [auth B]
BA [auth G],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
R [auth D],
S [auth D],
U [auth E],
V [auth E],
X [auth F],
Y [auth F],
Z [auth G]
HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 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: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-04-15
    Changes: Database references
  • Version 1.2: 2020-04-22
    Changes: Database references