5YYS | pdb_00005yys

Cryo-EM structure of L-fucokinase, GDP-fucose pyrophosphorylase (FKP)in Bacteroides fragilis

• PDB DOI: https://doi.org/10.2210/pdb5YYS/pdb
• EM Map EMD-6859: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Bacteroides fragilis
• Mutation(s): No 


• Deposited: 2017-12-11 Released: 2018-12-12 
• Deposition Author(s): Wang, J., Hu, H., Liu, Y., Zhou, Q., Wu, P., Yan, N., Wang, H.W., Wu, J.W., Sun, L.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of L-fucokinase/GDP-fucose pyrophosphorylase (FKP) in Bacteroides fragilis.

Liu, Y., Hu, H., Wang, J., Zhou, Q., Wu, P., Yan, N., Wang, H.W., Wu, J.W., Sun, L.

(2019) Protein Cell 10: 365-369

• PubMed: 30242642 
• DOI: https://doi.org/10.1007/s13238-018-0576-x
• Primary Citation of Related Structures:  
  5YYS

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Organizational Affiliation: 
• Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
School of Life Sciences, Tsinghua University, Beijing, 100084, China.
State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 423.13 kDa 
• Atom Count: 24,044 
• Modeled Residue Count: 3,244 
• Deposited Residue Count: 3,796 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-fucokinase, L-fucose-1-P guanylyltransferase	A, B, C, D	949	Bacteroides fragilis	Mutation(s): 0  EC: 2.7.1.52 (UniProt), 2.7.7.30 (UniProt)
UniProt
Find proteins for Q58T34 (Bacteroides fragilis) Explore Q58T34  Go to UniProtKB:  Q58T34

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Wang, J., Hu, H., Liu, Y., Zhou, Q., Wu, P., Yan, N., Wang, H.W., Wu, J.W., Sun, L.

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2019-05-01
  Changes: Data collection, Database references
• Version 1.2: 2019-11-06
  Changes: Data collection, Other
• Version 1.3: 2024-03-27
  Changes: Data collection, Database references
• Version 1.4: 2025-07-02
  Changes: Data collection, Structure summary