5FFM | pdb_00005ffm

Yellow fever virus helicase

• PDB DOI: https://doi.org/10.2210/pdb5FFM/pdb
• Entry: 5FFM supersedes: 1YMF

• Classification: HYDROLASE
• Organism(s): Yellow fever virus 17D
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-12-18 Released: 2015-12-30 
• Deposition Author(s): Smith, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.250 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Structure of the Flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing.

Wu, J., Bera, A.K., Kuhn, R.J., Smith, J.L.

(2005) J Virol 79: 10268-10277

• PubMed: 16051820 
• DOI: https://doi.org/10.1128/JVI.79.16.10268-10277.2005
• Primary Citation Related Structures: 
  1YKS, 5FFM


• PubMed Abstract: 
  

  Yellow fever virus (YFV), a member of the Flavivirus genus, has a plus-sense RNA genome encoding a single polyprotein. Viral protein NS3 includes a protease and a helicase that are essential to virus replication and to RNA capping. The 1.8-A crystal structure of the helicase region of the YFV NS3 protein includes residues 187 to 623. Two familiar helicase domains bind nucleotide in a triphosphate pocket without base recognition, providing a site for nonspecific hydrolysis of nucleoside triphosphates and RNA triphosphate. The third, C-terminal domain has a unique structure and is proposed to function in RNA and protein recognition. The organization of the three domains indicates that cleavage of the viral polyprotein NS3-NS4A junction occurs in trans.

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Organizational Affiliation: 
• Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 50.01 kDa 
• Atom Count: 3,314 
• Modeled Residue Count: 417 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease NS3	A	440	Yellow fever virus 17D	Mutation(s): 0  EC: 3.4.21.91
UniProt
Find proteins for P03314 (Yellow fever virus (strain 17D vaccine)) Explore P03314  Go to UniProtKB:  P03314

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.250 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.66	α = 90
b = 44.37	β = 104.09
c = 92.51	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-30 
Deposition Author(s): Smith, J.L.
• This entry supersedes: 1YMF

Revision History  

• Version 1.0: 2015-12-30
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-10-30
  Changes: Structure summary