5YXA

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 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

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.

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 
• Modelled 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 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• 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