1SFK | pdb_00001sfk

Core (C) protein from West Nile Virus, subtype Kunjin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.311 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.249 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.252 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

West nile virus core protein; tetramer structure and ribbon formation

Dokland, T., Walsh, M., Mackenzie, J.M., Khromykh, A.A., Ee, K.-H., Wang, S.

(2004) Structure 12: 1157-1163

  • DOI: https://doi.org/10.1016/j.str.2004.04.024
  • Primary Citation of Related Structures:  
    1SFK

  • PubMed Abstract: 

    We have determined the crystal structure of the core (C) protein from the Kunjin subtype of West Nile virus (WNV), closely related to the NY99 strain of WNV, currently a major health threat in the U.S. WNV is a member of the Flaviviridae family of enveloped RNA viruses that contains many important human pathogens. The C protein is associated with the RNA genome and forms the internal core which is surrounded by the envelope in the virion. The C protein structure contains four alpha helices and forms dimers that are organized into tetramers. The tetramers form extended filamentous ribbons resembling the stacked alpha helices seen in HEAT protein structures.

    • Organizational Affiliation: 
    • Institute of Molecular and Cell Biology, Singapore, Republic of Singapore. dokland@uab.edu

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Core protein
A, B, C, D, E
A, B, C, D, E, F, G, H
76Kunjin virus (STRAIN MRM61C)Mutation(s): 0 
UniProt
Find proteins for P14335 (Kunjin virus (strain MRM61C))
Explore P14335 
Go to UniProtKB:  P14335
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14335
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4
Download Ideal Coordinates CCD File 
L [auth A],
O [auth D],
R [auth F],
U [auth G]		TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PO4
Query on PO4
Download Ideal Coordinates CCD File 
K [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA
Query on CA
Download Ideal Coordinates CCD File 
I [auth A],
M [auth D],
P [auth F],
S [auth G]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
J [auth A],
N [auth D],
Q [auth F],
T [auth G]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.311 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.249 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.252 (Depositor) 
Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.655α = 90
b = 85.655β = 90
c = 214.384γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations, Refinement description