8WLK

Cryo-EM structure of human VMAT2 in presence of Tetrabenazine, determined in an outward-facing conformation

• PDB DOI: https://doi.org/10.2210/pdb8WLK/pdb
• EM Map EMD-37622: EMDB EMDataResource

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


• Deposited: 2023-09-30 Released: 2024-06-12 
• Deposition Author(s): Qu, Q., Wang, Y., Zhou, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.37 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of human apo VMAT2 in an outward-facing conformation

Qu, Q., Wang, Y., Zhou, Z.

To be published.

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: 54.14 kDa 
• Atom Count: 2,873 
• Modelled Residue Count: 383 
• Deposited Residue Count: 497 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptic vesicular amine transporter	A	497	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EBZ (Subject of Investigation/LOI)	B [auth A]	(3S,5R,11bS)-9,10-dimethoxy-3-(2-methylpropyl)-1,3,4,6,7,11b-hexahydro-2H-pyrido[2,1-a]isoquinolin-2-one C19 H27 N O3 MKJIEFSOBYUXJB-HOCLYGCPSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EBZ	BindingDB:  8WLK	Ki: min: 4, max: 3.64e+4 (nM) from 5 assay(s)
		Kd: min: 2, max: 100 (nM) from 6 assay(s)
		IC50: min: 8.3, max: 200 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.37 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Qu, Q., Wang, Y., Zhou, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171194

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release