4N5B

Crystal structure of the Nipah virus phosphoprotein tetramerization domain

• PDB DOI: https://doi.org/10.2210/pdb4N5B/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Henipavirus nipahense
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-09 Released: 2013-11-27 
• Deposition Author(s): Bruhn, J.F., Barnett, K., Bibby, J., Thomas, J., Keegan, R., Rigden, D., Bornholdt, Z.A., Saphire, E.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the nipah virus phosphoprotein tetramerization domain.

Bruhn, J.F., Barnett, K.C., Bibby, J., Thomas, J.M., Keegan, R.M., Rigden, D.J., Bornholdt, Z.A., Saphire, E.O.

(2014) J Virol 88: 758-762

• PubMed: 24155387 
• DOI: https://doi.org/10.1128/JVI.02294-13
• Primary Citation of Related Structures:  
  4N5B


• PubMed Abstract: 
  

  The Nipah virus phosphoprotein (P) is multimeric and tethers the viral polymerase to the nucleocapsid. We present the crystal structure of the multimerization domain of Nipah virus P: a long, parallel, tetrameric, coiled coil with a small, α-helical cap structure. Across the paramyxoviruses, these domains share little sequence identity yet are similar in length and structural organization, suggesting a common requirement for scaffolding or spatial organization of the functions of P in the virus life cycle.

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Organizational Affiliation: 

Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 102.43 kDa 
• Atom Count: 7,506 
• Modelled Residue Count: 813 
• Deposited Residue Count: 880 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoprotein	A, B [auth E], C [auth D], D [auth C], E [auth H], F, G [auth B], H [auth G]	110	Henipavirus nipahense	Mutation(s): 0  Gene Names: P/V/W/C
UniProt
Find proteins for D2DEB8 (Nipah virus) Explore D2DEB8  Go to UniProtKB:  D2DEB8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	AA [auth B], BA [auth G], CA [auth G], I [auth A], J [auth A], K [auth A], L [auth E], M [auth E], N [auth E], O [auth D], P [auth D], Q [auth D], R [auth C], S [auth H], T [auth H], U [auth H], V [auth H], W [auth F], X [auth B], Y [auth B], Z [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.061	α = 100.56
b = 76.877	β = 100.85
c = 80.748	γ = 107.78

Software Package:

Software Name	Purpose
Web-Ice	data collection
AMPLE	phasing
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-27 
Deposition Author(s): Bruhn, J.F., Barnett, K., Bibby, J., Thomas, J., Keegan, R., Rigden, D., Bornholdt, Z.A., Saphire, E.O.

Revision History  

• Version 1.0: 2013-11-27
  Type: Initial release
  
• Version 1.1: 2014-01-15
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description