9KOM | pdb_00009kom

Cryo-EM structure of human pannexin-3 protomer

• PDB DOI: https://doi.org/10.2210/pdb9KOM/pdb
• EM Map EMD-62478: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2024-11-20 Released: 2025-01-15 
• Deposition Author(s): Tsuyama, T., Yokoyama, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Cryo-EM structure of the human Pannexin-3 channel.

Tsuyama, T., Teramura, R., Mitsuoka, K., Kishikawa, J.I., Yokoyama, K.

(2025) Biochem Biophys Res Commun 745: 151227-151227

• PubMed: 39721314 
• DOI: https://doi.org/10.1016/j.bbrc.2024.151227
• Primary Citation of Related Structures:  
  9KOM, 9KRG


• PubMed Abstract: 
  

  Pannexin-3 (PANX3) is a member of the pannexin family of large-pore, ATP-permeable channels conserved across vertebrates. PANX3 contributes to various developmental and pathophysiological processes by permeating ATP and Ca ²⁺ ions; however, the structural basis of PANX3 channel function remains unclear. Here, we present the cryo-EM structure of human PANX3 at 2.9-3.2 Å. The PANX3 channel is heptameric and forms a transmembrane pore along the central symmetric axis. The narrowest constriction of the pore is composed of an isoleucine ring located in the extracellular region, and its size is comparable to that of other pannexins. A structural variability analysis revealed prominent structural dynamics in intracellular regions. Our structural studies provide a foundation for understanding the detailed properties of pannexin channels.

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Organizational Affiliation: 
• Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, 603-8555, Japan.
Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Osaka, Japan.
Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, 603-8555, Japan; Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan.
Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, 603-8555, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 45.97 kDa 
• Atom Count: 2,268 
• Modeled Residue Count: 291 
• Deposited Residue Count: 404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pannexin-3	A	404	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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1
RECONSTRUCTION	cryoSPARC	4.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Tsuyama, T., Yokoyama, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	23H02453
Japan Society for the Promotion of Science (JSPS)	Japan	20J01396
Japan Society for the Promotion of Science (JSPS)	Japan	20K06514
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	--

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release