5FVA | pdb_00005fva

Toscana Virus Nucleocapsid Protein

PDB DOI: https://doi.org/10.2210/pdb5FVA/pdb

Classification: VIRAL PROTEIN
Organism(s): Toscana virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-02-03 Released: 2016-03-09
Deposition Author(s): Baklouti, A., Sevajol, M., Goulet, A., Lichiere, J., Ferron, F., Canard, B., Charrel, R.N., Coutard, B., Papageorgiou, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.70 Å
R-Value Free:
0.271 (Depositor), 0.272 (DCC)
R-Value Work:
0.228 (Depositor), 0.227 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Toscana virus nucleoprotein oligomer organization observed in solution.

Baklouti, A., Goulet, A., Lichiere, J., Canard, B., Charrel, R.N., Ferron, F., Coutard, B., Papageorgiou, N.

(2017) Acta Crystallogr D Struct Biol 73: 650-659

PubMed: 28777080 Search on PubMed
DOI: https://doi.org/10.1107/S2059798317008774
Primary Citation Related Structures:
5FVA

PubMed Abstract:
Toscana virus (TOSV) is an arthropod-borne virus belonging to the Phlebovirus genus within the Bunyaviridae family. As in other bunyaviruses, the genome of TOSV is made up of three RNA segments. They are encapsidated by the nucleoprotein (N), which also plays an essential role in virus replication. To date, crystallographic structures of phlebovirus N have systematically revealed closed-ring organizations which do not fully match the filamentous organization of the ribonucleoprotein (RNP) complex observed by electron microscopy. In order to further bridge the gap between crystallographic data on N and observations of the RNP by electron microscopy, the structural organization of recombinant TOSV N was investigated by an integrative approach combining X-ray diffraction crystallography, transmission electron microscopy, small-angle X-ray scattering, size-exclusion chromatography and multi-angle laser light scattering. It was found that in solution TOSV N forms open oligomers consistent with the encapsidation mechanism of phlebovirus RNA.

Organizational Affiliation

Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France.

Macromolecule Content

Total Structure Weight: 166.11 kDa
Atom Count: 9,625
Modeled Residue Count: 1,452
Deposited Residue Count: 1,518
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEOPROTEIN	A, B, C, D, E A, B, C, D, E, F	253	Toscana virus	Mutation(s): 0
UniProt
Find proteins for P21701 (Toscana virus) Explore P21701 Go to UniProtKB: P21701
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21701
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth F] SDF format, chain J [auth E] SDF format, chain I [auth D] SDF format, chain H [auth C] SDF format, chain G [auth A] MOL2 format, chain K [auth F] MOL2 format, chain J [auth E] MOL2 format, chain I [auth D] MOL2 format, chain H [auth C] MOL2 format, chain G [auth A] mmCIF format, chain K [auth F] mmCIF format, chain J [auth E] mmCIF format, chain I [auth D] mmCIF format, chain H [auth C] mmCIF format, chain G [auth A]	G [auth A], H [auth C], I [auth D], J [auth E], K [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth E] Focus chain K [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth E] Focus chain K [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.70 Å
R-Value Free: 0.271 (Depositor), 0.272 (DCC)
R-Value Work: 0.228 (Depositor), 0.227 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.615	α = 90
b = 174.615	β = 90
c = 89.824	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-03-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-03-09
Type: Initial release
Version 1.1: 2016-03-16
Changes: Database references
Version 1.2: 2017-08-09
Changes: Database references
Version 1.3: 2017-08-23
Changes: Database references
Version 1.4: 2024-01-10
Changes: Data collection, Database references, Other, Refinement description