8XOB | pdb_00008xob

VMAT2 protonated state

• PDB DOI: https://doi.org/10.2210/pdb8XOB/pdb
• EM Map EMD-38525: EMDB EMDataResource

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


• Deposited: 2023-12-31 Released: 2024-05-08 
• Deposition Author(s): Jiang, D.H., Wu, D.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural snapshots of human VMAT2 reveal insights into substrate recognition and proton coupling mechanism.

Wu, D., Yu, Z., Chen, Q., Zhao, J., Huang, B., Wang, Y., Su, J., Li, N., Jiang, D., Zhao, Y.

(2024) Cell Res 34: 586-589

• PubMed: 38777861 
• DOI: https://doi.org/10.1038/s41422-024-00974-9
• Primary Citation Related Structures: 
  8JSX, 8JT5, 8JTB, 8XO9, 8XOA, 8XOB

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Organizational Affiliation: 
• Institute of Physics, Chinese Academy of Sciences, Beijing, China.
University of Chinese Academy of Sciences, Beijing, China.
Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China.
Beijing StoneWise Technology Co., Ltd, Beijing, China.
Heart Center and Beijing Key Laboratory of Hypertension, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China.
Institute of Physics, Chinese Academy of Sciences, Beijing, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 61.93 kDa 
• Atom Count: 2,858 
• Modeled Residue Count: 387 
• Deposited Residue Count: 573 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptic vesicular amine transporter,transporter B	A	573	Homo sapiens	Mutation(s): 0  Gene Names: SLC18A2, SVMT, VMAT2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q05940 (Homo sapiens) Explore Q05940  Go to UniProtKB:  Q05940
PHAROS:  Q05940 GTEx:  ENSG00000165646

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): Jiang, D.H., Wu, D.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2025-07-02
  Changes: Data collection