9OQM | pdb_00009oqm

Apo class from combined 0, 10, 20, 30 mM ATP datastes

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2025-05-21 Released: 2025-12-24 
  • Deposition Author(s): Ruan, Z., Li, Y., Du, J., Lu, W.
  • Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9OQM

This is version 1.0 of the entry. See complete history

Literature

Structural basis of PANX1 permeation and positive modulation by mefloquine.

Li, Y.Ruan, Z.Lee, J.Orozco, I.J.Zhou, E.Du, J.Lu, W.

(2025) Nat Commun 16: 11057-11057

  • DOI: https://doi.org/10.1038/s41467-025-66028-9
  • Primary Citation Related Structures: 
    9OQG, 9OQH, 9OQI, 9OQJ, 9OQK, 9OQL, 9OQM, 9OQN, 9OQO, 9OQP, 9OQQ

  • PubMed Abstract: 

    Purinergic signaling relies on ATP release through exocytosis and large-pore channels. Large-pore channels permeate both small anions like chloride and large signaling molecules like ATP, but how this broad cargo selectivity is structurally controlled remains elusive. Here we investigate PANX1, a prototypical large-pore channel, and uncover structural plasticity at the extracellular entrance formed by seven tryptophan (W74) residues. The W74 sidechains are flexible, sampling conformations that range from a constricted state permissive only to chloride to a dilated state compatible with ATP. These states are coupled to variable cation-π interactions between W74 and arginine 75 (R75), suggesting a mechanism for dynamic tuning of pore architecture and selective cargo permeation. We also identify mefloquine as a positive modulator of PANX1 that binds near the side tunnel to control ion flow through this pathway. Together, these findings define the structural principles underlying PANX1 permeation and modulation.


  • Organizational Affiliation
    • Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.

Macromolecule Content 

  • Total Structure Weight: 348.76 kDa 
  • Atom Count: 18,970 
  • Modeled Residue Count: 2,408 
  • Deposited Residue Count: 2,982 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q96RD7-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PTY
(Subject of Investigation/LOI)

Query on PTY



Download:Ideal Coordinates CCD File
BA [auth F]
FA [auth G]
H [auth A]
L [auth B]
P [auth C]
BA [auth F],
FA [auth G],
H [auth A],
L [auth B],
P [auth C],
T [auth D],
X [auth E]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
CA [auth F]
DA [auth F]
GA [auth G]
HA [auth G]
I [auth A]
CA [auth F],
DA [auth F],
GA [auth G],
HA [auth G],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
Q [auth C],
R [auth C],
U [auth D],
V [auth D],
Y [auth E],
Z [auth E]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth E]
EA [auth F]
IA [auth G]
K [auth A]
O [auth B]
AA [auth E],
EA [auth F],
IA [auth G],
K [auth A],
O [auth B],
S [auth C],
W [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR00NS128258
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01HL153219
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS112363
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM138321
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS111031
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS129804

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release