8XLI | pdb_00008xli

Structure of the Vo sector of V-ATPase in the adult cortex and hippocampus

• PDB DOI: https://doi.org/10.2210/pdb8XLI/pdb
• EM Map EMD-38449: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus
• Mutation(s): No 


• Deposited: 2023-12-26 Released: 2025-07-02 
• Deposition Author(s): Zhang, M., Feng, J., Li, Y., Zhu, S.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: TISSUE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the Vo sector of V-ATPase in the adult cortex and hippocampus

Zhang, M., Feng, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 16-mer - A9B1C1D1E1F1G1H1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 16-mer - A10B1C1D1E1F1G1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 342.6 kDa 
• Atom Count: 23,024 
• Modeled Residue Count: 3,075 
• Deposited Residue Count: 3,142 
• Unique protein chains: 8

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase 116 kDa subunit a 1	A [auth a]	828	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P25286 (Rattus norvegicus) Explore P25286  Go to UniProtKB:  P25286

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a	B [auth b]	203	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for B0K022 (Rattus norvegicus) Explore B0K022  Go to UniProtKB:  B0K022

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit S1	C [auth c]	204	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for O54715 (Rattus norvegicus) Explore O54715  Go to UniProtKB:  O54715
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: O54715-1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit	D [auth d]	342	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q5M7T6 (Rattus norvegicus) Explore Q5M7T6  Go to UniProtKB:  Q5M7T6

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit e 2	E [auth e]	77	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q5EB76 (Rattus norvegicus) Explore Q5EB76  Go to UniProtKB:  Q5EB76

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease K	F [auth f]	89	Rattus norvegicus	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase 16 kDa proteolipid subunit c	G [auth g], H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], M [auth m], N [auth n], O [auth o]	150	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P63081 (Rattus norvegicus) Explore P63081  Go to UniProtKB:  P63081

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Renin receptor cytoplasmic fragment	P [auth p]	49	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q6AXS4 (Rattus norvegicus) Explore Q6AXS4  Go to UniProtKB:  Q6AXS4

Oligosaccharides

Help

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	Q [auth A], R [auth B], S [auth C], T [auth D]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: TISSUE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Zhang, M., Feng, J., Li, Y., Zhu, S.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release