9W8D | pdb_00009w8d

human VMAT2 in complex with MDMA

PDB DOI: https://doi.org/10.2210/pdb9W8D/pdb
EM Map EMD-65744: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-08-07 Released: 2026-10-07
Deposition Author(s): Wu, D., Jiang, D.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.89 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9W8D

This is version 1.0 of the entry. See complete history.

Literature

transporter C with 3

Wu, D., Jiang, D.H.

To be published.

Macromolecule Content

Total Structure Weight: 55.94 kDa
Atom Count: 2,865
Modeled Residue Count: 385
Deposited Residue Count: 514
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptic vesicular amine transporter	A	514	Homo sapiens	Mutation(s): 0 Gene Names: SLC18A2, SVMT, VMAT2
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q05940
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B41 (Subject of Investigation/LOI) Query on B41 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]	(2S)-1-(1,3-benzodioxol-5-yl)-N-methylpropan-2-amine C₁₁ H₁₅ N O₂ SHXWCVYOXRDMCX-QMMMGPOBSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.89 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.16_3549
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31971134

Revision History (Full details and data files)

Version 1.0: 2026-10-07
Type: Initial release