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- PDB-5fva: Toscana Virus Nucleocapsid Protein -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5fva
TitleToscana Virus Nucleocapsid Protein
ComponentsNUCLEOPROTEIN
KeywordsVIRAL PROTEIN / TOSCANA VIRUS / NUCLEOCAPSIDE / NUCLEOPROTEIN / PHLEBOVIRUS / RNA VIRUS / BUNYAVIRIDAE
Function / homology
Function and homology information


helical viral capsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / host cell nucleus / RNA binding
Similarity search - Function
Nucleocapsid, Phlebovirus/Tenuivirus / Nucleocapsid, Phlebovirus / Tenuivirus/Phlebovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesTOSCANA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsBaklouti, A. / Sevajol, M. / Goulet, A. / Lichiere, J. / Ferron, F. / Canard, B. / Charrel, R.N. / Coutard, B. / Papageorgiou, N.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Toscana virus nucleoprotein oligomer organization observed in solution.
Authors: Baklouti, A. / Goulet, A. / Lichiere, J. / Canard, B. / Charrel, R.N. / Ferron, F. / Coutard, B. / Papageorgiou, N.
History
DepositionFeb 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Aug 9, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.3Aug 23, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEOPROTEIN
B: NUCLEOPROTEIN
C: NUCLEOPROTEIN
D: NUCLEOPROTEIN
E: NUCLEOPROTEIN
F: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,11111
Polymers165,9966
Non-polymers1155
Water543
1
C: NUCLEOPROTEIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)166,13412
Polymers165,9966
Non-polymers1386
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_255-x+y-3,-x,z1
crystal symmetry operation6_675x-y+1,x+2,z1
crystal symmetry operation4_375-x-2,-y+2,z1
crystal symmetry operation2_585-y,x-y+3,z1
crystal symmetry operation5_345y-2,-x+y-1,z1
Buried area20010 Å2
ΔGint-171.4 kcal/mol
Surface area72570 Å2
MethodPISA
2
A: NUCLEOPROTEIN
B: NUCLEOPROTEIN
hetero molecules

A: NUCLEOPROTEIN
B: NUCLEOPROTEIN
hetero molecules

A: NUCLEOPROTEIN
B: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,0659
Polymers165,9966
Non-polymers693
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_695-y+1,x-y+4,z1
crystal symmetry operation3_265-x+y-3,-x+1,z1
Buried area14270 Å2
ΔGint-142.8 kcal/mol
Surface area71690 Å2
MethodPISA
3
D: NUCLEOPROTEIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)166,13412
Polymers165,9966
Non-polymers1386
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_255-x+y-3,-x,z1
crystal symmetry operation4_375-x-2,-y+2,z1
crystal symmetry operation6_675x-y+1,x+2,z1
crystal symmetry operation2_585-y,x-y+3,z1
crystal symmetry operation5_345y-2,-x+y-1,z1
Buried area9030 Å2
ΔGint-85.4 kcal/mol
Surface area73820 Å2
MethodPISA
4
E: NUCLEOPROTEIN
F: NUCLEOPROTEIN
hetero molecules

E: NUCLEOPROTEIN
F: NUCLEOPROTEIN
hetero molecules

E: NUCLEOPROTEIN
F: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,13412
Polymers165,9966
Non-polymers1386
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_695-y+1,x-y+4,z1
crystal symmetry operation3_265-x+y-3,-x+1,z1
Buried area9530 Å2
ΔGint-103.2 kcal/mol
Surface area75670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.615, 174.615, 89.824
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein
NUCLEOPROTEIN / / NUCLEOCAPSID PROTEIN / PROTEIN N / TOSCANA VIRUS NUCLEOCPSIDE PROTEIN


Mass: 27665.967 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOSCANA VIRUS / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P21701
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.9 % / Description: NONE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.965
DetectorType: EIGER 4M / Detector: PIXEL / Date: Jan 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.46
ReflectionResolution: 3.7→48.22 Å / Num. obs: 18291 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 10.48
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 1.99 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB MODEL 4CSG

4csg


Resolution: 3.7→48.222 Å / σ(F): 1.36 / Phase error: 26.32 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2714 3277 10.03 %
Rwork0.2281 --
obs0.2341 32686 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Refinement stepCycle: LAST / Resolution: 3.7→48.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9617 0 5 3 9625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079771
X-RAY DIFFRACTIONf_angle_d1.47713449
X-RAY DIFFRACTIONf_dihedral_angle_d13.0753027
X-RAY DIFFRACTIONf_chiral_restr0.0571691
X-RAY DIFFRACTIONf_plane_restr0.0091771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7001-3.76380.35011640.27231450X-RAY DIFFRACTION90
3.7638-3.83220.31151590.28131433X-RAY DIFFRACTION90
3.8322-3.90590.35881620.26671513X-RAY DIFFRACTION90
3.9059-3.98560.30881600.2751474X-RAY DIFFRACTION90
3.9856-4.07220.32471600.25931438X-RAY DIFFRACTION90
4.0722-4.16680.30391700.25751496X-RAY DIFFRACTION90
4.1668-4.27090.33471720.25871501X-RAY DIFFRACTION90
4.2709-4.38630.30061620.25061438X-RAY DIFFRACTION90
4.3863-4.51520.29891600.23251459X-RAY DIFFRACTION90
4.5152-4.66080.30621660.2291456X-RAY DIFFRACTION90
4.6608-4.82720.30461700.24841477X-RAY DIFFRACTION90
4.8272-5.02020.321600.24761498X-RAY DIFFRACTION90
5.0202-5.24830.38491580.25661461X-RAY DIFFRACTION90
5.2483-5.52440.3031640.23431468X-RAY DIFFRACTION90
5.5244-5.86980.2671670.23361454X-RAY DIFFRACTION90
5.8698-6.32170.23691620.24231483X-RAY DIFFRACTION90
6.3217-6.95550.22161740.22351467X-RAY DIFFRACTION89
6.9555-7.95640.28761640.21551480X-RAY DIFFRACTION90
7.9564-10.00350.17421580.18531474X-RAY DIFFRACTION90
10.0035-43.05620.22061650.1981479X-RAY DIFFRACTION90

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