8WLM | pdb_00008wlm

Cryo-EM structure of human VMAT2 in presence of 5-HT, determined in an outward-facing conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 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

Transport and inhibition mechanism for VMAT2-mediated synaptic vesicle loading of monoamines.

Wang, Y.Zhang, P.Chao, Y.Zhu, Z.Yang, C.Zhou, Z.Li, Y.Long, Y.Liu, Y.Li, D.Wang, S.Qu, Q.

(2024) Cell Res 34: 47-57

  • DOI: https://doi.org/10.1038/s41422-023-00906-z
  • Primary Citation of Related Structures:  
    8WLJ, 8WLK, 8WLL, 8WLM

  • PubMed Abstract: 

    Monoamine neurotransmitters such as serotonin and dopamine are loaded by vesicular monoamine transporter 2 (VMAT2) into synaptic vesicles for storage and subsequent release in neurons. Impaired VMAT2 function underlies various neuropsychiatric diseases. VMAT2 inhibitors reserpine and tetrabenazine are used to treat hypertension, movement disorders associated with Huntington's Disease and Tardive Dyskinesia. Despite its physiological and pharmacological significance, the structural basis underlying VMAT2 substrate recognition and its inhibition by various inhibitors remains unknown. Here we present cryo-EM structures of human apo VMAT2 in addition to states bound to serotonin, tetrabenazine, and reserpine. These structures collectively capture three states, namely the lumen-facing, occluded, and cytosol-facing conformations. Notably, tetrabenazine induces a substantial rearrangement of TM2 and TM7, extending beyond the typical rocker-switch movement. These functionally dynamic snapshots, complemented by biochemical analysis, unveil the essential components responsible for ligand recognition, elucidate the proton-driven exchange cycle, and provide a framework to design improved pharmaceutics targeting VMAT2.


  • Organizational Affiliation
    • Shanghai Stomatological Hospital, School of Stomatology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptic vesicular amine transporter497Homo sapiensMutation(s): 0 
Gene Names: SLC18A2SVMTVMAT2
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05940
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
SRO BindingDB:  8WLM Ki: min: 2290, max: 6.40e+5 (nM) from 3 assay(s)
IC50: min: 98, max: 1430 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171194

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Data collection, Database references, Structure summary