5YXA | pdb_00005yxa

Crystal structure of the C-terminal fragment of NS1 protein from yellow fever virus

• PDB DOI: https://doi.org/10.2210/pdb5YXA/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Yellow fever virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-04 Released: 2018-01-24 
• Deposition Author(s): Wang, H., Song, H., Qi, J., Shi, Y., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the C-terminal fragment of NS1 protein from yellow fever virus.

Wang, H., Han, M., Qi, J., Hilgenfeld, R., Luo, T., Shi, Y., Gao, G.F., Song, H.

(2017) Sci China Life Sci 60: 1403-1406

• PubMed: 29285718 
• DOI: https://doi.org/10.1007/s11427-017-9238-8
• Primary Citation of Related Structures:  
  5YXA

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Organizational Affiliation: 
• Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning, 530004, China.
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
Institute of Biochemistry, Center for Structural and Cell Biology, University of Lübeck, Lübeck, 23562, Germany.
German Center for Infection Research (DZIF), Hamburg-Lübeck Borstel-Riems Site, University of Lübeck, Lübeck, 23562, Germany.
Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing, 100101, China.
Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518112, China.
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].
Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].
Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China. [e-mail].
Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518112, China. [e-mail].
Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].
National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China. [e-mail].
Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, 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 PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 79.93 kDa 
• Atom Count: 5,540 
• Modeled Residue Count: 708 
• Deposited Residue Count: 724 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 1	A, B, C, D	181	Yellow fever virus	Mutation(s): 0
UniProt
Find proteins for Q1X881 (Yellow fever virus (isolate Angola/14FA/1971)) Explore Q1X881  Go to UniProtKB:  Q1X881

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.291	α = 90
b = 114.104	β = 90
c = 139.215	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-24 
Deposition Author(s): Wang, H., Song, H., Qi, J., Shi, Y., Gao, G.F.

Revision History  

• Version 1.0: 2018-01-24
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Database references
• Version 1.2: 2018-02-07
  Changes: Structure summary
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary