4N5B | pdb_00004n5b

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.238 (Depositor), 0.236 (DCC)
R-Value Work:
0.187 (Depositor), 0.187 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/JVI.02294-13
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoprotein	A B [auth E] C [auth D] D [auth C] E [auth H] 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D2DEB8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth F] SDF format, chain V [auth H] SDF format, chain U [auth H] SDF format, chain T [auth H] SDF format, chain S [auth H] SDF format, chain R [auth C] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain N [auth E] SDF format, chain M [auth E] SDF format, chain L [auth E] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain CA [auth G] SDF format, chain BA [auth G] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth F] MOL2 format, chain V [auth H] MOL2 format, chain U [auth H] MOL2 format, chain T [auth H] MOL2 format, chain S [auth H] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain N [auth E] MOL2 format, chain M [auth E] MOL2 format, chain L [auth E] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain CA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth F] mmCIF format, chain V [auth H] mmCIF format, chain U [auth H] mmCIF format, chain T [auth H] mmCIF format, chain S [auth H] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain N [auth E] mmCIF format, chain M [auth E] mmCIF format, chain L [auth E] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain CA [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth G] CA [auth G] I [auth A] J [auth A] 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		Interactions Focus chain AA [auth B] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth C] Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth H] Focus chain V [auth H] Focus chain W [auth F] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth C] Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth H] Focus chain V [auth H] Focus chain W [auth F] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.238 (Depositor), 0.236 (DCC)
R-Value Work: 0.187 (Depositor), 0.187 (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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-11-27

Deposition Author(s):

Revision History (Full details and data files)

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