8ZMR | pdb_00008zmr

Vesamicol-bound VAChT

• PDB DOI: https://doi.org/10.2210/pdb8ZMR/pdb
• EM Map EMD-60254: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12, Homo sapiens, synthetic construct
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-05-23 Released: 2024-06-19 
• Deposition Author(s): Zhang, Z., Zhang, Y., Dai, F., Zhang, Y.X., Lee, C.-H.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into VAChT neurotransmitter recognition and inhibition.

Zhang, Y., Dai, F., Chen, N., Zhou, D., Lee, C.H., Song, C., Zhang, Y., Zhang, Z.

(2024) Cell Res 34: 665-668

• PubMed: 38862671 
• DOI: https://doi.org/10.1038/s41422-024-00986-5
• Primary Citation Related Structures: 
  8ZMR, 8ZMS

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Organizational Affiliation: 
• State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China.
Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA. [e-mail].
Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China. [e-mail].
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China. [e-mail].
Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China. [e-mail].
State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China. [e-mail].
State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China. [e-mail].
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China. [e-mail].

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: 112.96 kDa 
• Atom Count: 2,916 
• Modeled Residue Count: 384 
• Deposited Residue Count: 1,047 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,Vesicular acetylcholine transporter,DARPinoff7	A	1,047	Escherichia coli K-12, Homo sapiens, synthetic construct This entity is chimeric	Mutation(s): 1  Gene Names: malE, b4034, JW3994, SLC18A3, VACHT
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for Q16572 (Homo sapiens) Explore Q16572  Go to UniProtKB:  Q16572
PHAROS:  Q16572 GTEx:  ENSG00000187714
UniProt Groups	Q16572P0AEX9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1LWL	B [auth A]	vesamicol C17 H25 N O YSSBJODGIYRAMI-IRXDYDNUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Zhang, Z., Zhang, Y., Dai, F., Zhang, Y.X., Lee, C.-H.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release
  
• Version 1.1: 2024-09-18
  Changes: Data collection, Database references