8XIT

Cryo-EM structure of sheep VMAT2 dimer in an atypical fold

• PDB DOI: https://doi.org/10.2210/pdb8XIT/pdb
• EM Map EMD-38389: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Ovis aries
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2023-12-20 Released: 2024-08-14 
• Deposition Author(s): Lyu, Y., Fu, C., Ma, H., Sun, Z., Su, Z., Zhou, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Engineering of a mammalian VMAT2 for cryo-EM analysis results in non-canonical protein folding.

Lyu, Y., Fu, C., Ma, H., Su, Z., Sun, Z., Zhou, X.

(2024) Nat Commun 15: 6511-6511

• PubMed: 39095428 
• DOI: https://doi.org/10.1038/s41467-024-50934-5
• Primary Citation of Related Structures:  
  8XIT, 8XIU


• PubMed Abstract: 
  

  Vesicular monoamine transporter 2 (VMAT2) belongs to the major facilitator superfamily (MFS), and mediates cytoplasmic monoamine packaging into presynaptic vesicles. Here, we present two cryo-EM structures of VMAT2, with a frog VMAT2 adopting a canonical MFS fold and an engineered sheep VMAT2 adopting a non-canonical fold. Both VMAT2 proteins mediate uptake of a selective fluorescent VMAT2 substrate into cells. Molecular docking, substrate binding and transport analysis reveal potential substrate binding mechanism in VMAT2. Meanwhile, caution is advised when interpreting engineered membrane protein structures.

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Organizational Affiliation: 

Department of Integrated Traditional Chinese and Western Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 137.19 kDa 
• Atom Count: 6,002 
• Modelled Residue Count: 784 
• Deposited Residue Count: 1,260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OaVMAT2-BRIL	A, B	630	Ovis aries	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.3
MODEL REFINEMENT	PHENIX	1.19.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-14 
Deposition Author(s): Lyu, Y., Fu, C., Ma, H., Sun, Z., Su, Z., Zhou, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31770783

Revision History  

• Version 1.0: 2024-08-14
  Type: Initial release