7WHR | pdb_00007whr

Cryo-EM Structure of Leishmanial GDP-mannose pyrophosphorylase

• PDB DOI: https://doi.org/10.2210/pdb7WHR/pdb
• EM Map EMD-32509: EMDB EMDataResource

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Leishmania donovani
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-12-31 Released: 2022-09-21 
• Deposition Author(s): Xu, W., Li, H., Huang, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into selective inhibition of leishmanial GDP-mannose pyrophosphorylase.

Li, H., Ji, T., Sun, Q., Chen, Y., Xu, W., Huang, C.

(2022) Cell Discov 8: 83-83

• PubMed: 36038534 
• DOI: https://doi.org/10.1038/s41421-022-00424-z
• Primary Citation of Related Structures:  
  7WHR, 7WHS, 7WHT

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Organizational Affiliation: 
• Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, Nanchang, Jiangxi, China.
Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China. [e-mail].
Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 250.68 kDa 
• Atom Count: 16,914 
• Modeled Residue Count: 2,184 
• Deposited Residue Count: 2,274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleotidyl transferase family protein	A [auth B], B [auth A], C, D, E, F	379	Leishmania donovani	Mutation(s): 0  Gene Names: CGC21_17635 EC: 2.7.7.13
UniProt
Find proteins for E9BG32 (Leishmania donovani) Explore E9BG32  Go to UniProtKB:  E9BG32

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-21 
Deposition Author(s): Xu, W., Li, H., Huang, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31971144
National Natural Science Foundation of China (NSFC)	China	31770807

Revision History  

• Version 1.0: 2022-09-21
  Type: Initial release
  
• Version 1.1: 2024-06-26
  Changes: Data collection
• Version 1.2: 2025-07-02
  Changes: Data collection, Structure summary