2IC6

The Coiled-coil Domain (residues 1-75) Structure of the Sin Nombre Virus Nucleocapsid Protein

• PDB DOI: https://doi.org/10.2210/pdb2IC6/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Orthohantavirus sinnombreense
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-09-12 Released: 2007-02-27 
• Deposition Author(s): Boudko, S.P., Rossmann, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.177 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 

Literature

The Coiled-coil Domain Structure of the Sin Nombre Virus Nucleocapsid Protein.

Boudko, S.P., Kuhn, R.J., Rossmann, M.G.

(2007) J Mol Biol 366: 1538-1544

• PubMed: 17222867 
• DOI: https://doi.org/10.1016/j.jmb.2006.12.046
• Primary Citation of Related Structures:  
  2IBL, 2IC6, 2IC9


• PubMed Abstract: 
  

  Hantaviruses can cause hemorrhagic fever with a renal syndrome and hantavirus pulmonary syndrome when transmitted to humans. The nucleocapsid protein of hantaviruses encapsidates viral genomic RNA and associates with transcription and replication complexes. Both the amino and carboxy termini of the nucleocapsid protein had been predicted to form trimers prior to the formation of the ribonucleoprotein. Crystal structures of amino-terminal fragments of the nucleocapsid protein showed the formation of intramolecular antiparallel coiled coils, but not intermolecular trimers. Thus, the amino-terminal part of the nucleocapsid protein is probably insufficient to initiate the trimerization of the full-length molecule.

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Organizational Affiliation: 

Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-2054, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.42 kDa 
• Atom Count: 1,429 
• Modelled Residue Count: 147 
• Deposited Residue Count: 156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleocapsid protein	A, B	78	Orthohantavirus sinnombreense	Mutation(s): 1  Gene Names: nucleocapsid protein EC: 3.1
UniProt
Find proteins for Q89462 (Sin Nombre orthohantavirus) Explore Q89462  Go to UniProtKB:  Q89462

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.177 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.116	α = 90
b = 49.521	β = 90
c = 100.554	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-27 
Deposition Author(s): Boudko, S.P., Rossmann, M.G.

Revision History  

• Version 1.0: 2007-02-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references
• Version 1.5: 2024-02-21
  Changes: Data collection