8GYP | pdb_00008gyp

Cryo-EM structure of human Pannexin-3 in closed state.

PDB DOI: https://doi.org/10.2210/pdb8GYP/pdb
EM Map EMD-34375: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2022-09-23 Released: 2024-04-17
Deposition Author(s): Cong, Y., Jin, X., Kong, F., Yan, C.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8GYP

This is version 1.2 of the entry. See complete history.

Literature

Inner channel lipids regulated gating mechanism of human pannexins.

Cong, Y., Jin, X., Kong, F., Yan, C.

To be published.

Macromolecule Content

Total Structure Weight: 314.69 kDa
Atom Count: 19,538
Modeled Residue Count: 2,450
Deposited Residue Count: 2,744
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pannexin-3	A, B, C, D, E A, B, C, D, E, F, G	392	Homo sapiens	Mutation(s): 0 Gene Names: PANX3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QZ0 (Homo sapiens) Explore Q96QZ0 Go to UniProtKB: Q96QZ0
PHAROS: Q96QZ0 GTEx: ENSG00000154143
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96QZ0
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G	Go to GlyGen: Q96QZ0-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain M [auth F] SDF format, chain N [auth G] SDF format, chain L [auth E] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain I [auth B] SDF format, chain H [auth A] MOL2 format, chain M [auth F] MOL2 format, chain N [auth G] MOL2 format, chain L [auth E] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] mmCIF format, chain M [auth F] mmCIF format, chain N [auth G] mmCIF format, chain L [auth E] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A]	H [auth A] I [auth B] J [auth C] K [auth D] L [auth E] H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth F] Focus chain N [auth G] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth F] Focus chain N [auth G]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2020YFA0509301

Revision History (Full details and data files)

Version 1.0: 2024-04-17
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Structure summary
Version 1.2: 2025-05-14
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.