8XIT | pdb_00008xit

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 
• Membrane Protein: Yes  PDBTMmpstruc


• 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.
State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China. [e-mail].
Department of Integrated Traditional Chinese and Western Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China. [e-mail].
Department of Integrated Traditional Chinese and Western Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China. [e-mail].

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 
• Modeled 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  Membrane Entity: Yes
UniProt
Find proteins for A0A6P7DBQ8 (Ovis aries) Explore A0A6P7DBQ8  Go to UniProtKB:  A0A6P7DBQ8

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