8JSX | pdb_00008jsx

VMAT2 complex with noradrenaline in lumen-facing state

PDB DOI: https://doi.org/10.2210/pdb8JSX/pdb
EM Map EMD-36629: EMDB EMDataResource

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

Deposited: 2023-06-20 Released: 2024-05-08
Deposition Author(s): Jiang, D.H., Wu, D.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.16 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-024-00974-9
Primary Citation of Related Structures:
8JSX, 8JT5, 8JTB, 8XO9, 8XOA, 8XOB

Organizational Affiliation

Institute of Physics, Chinese Academy of Sciences, Beijing, China.

Macromolecule Content

Total Structure Weight: 49.26 kDa
Atom Count: 2,828
Modelled Residue Count: 378
Deposited Residue Count: 457
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptic vesicular amine transporter	A	457	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05940
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E5E (Subject of Investigation/LOI) Query on E5E Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	Noradrenaline C₈ H₁₂ N O₃ SFLSHLFXELFNJZ-QMMMGPOBSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.16 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-08

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32271272

Revision History (Full details and data files)

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

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.