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- PDB-5ooo: Structure of the Rift Valley fever virus NSs protein core domain -

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Basic information

Entry
Database: PDB / ID: 5ooo
TitleStructure of the Rift Valley fever virus NSs protein core domain
ComponentsNon-structural protein NS-S
KeywordsVIRAL PROTEIN / Non-structural protein / interferon antagonist / virulence factor
Function / homology
Function and homology information


symbiont-mediated suppression of host transcription initiation from RNA polymerase II promoter / symbiont-mediated suppression of host transcription / suppression by virus of host type I interferon production / symbiont-mediated suppression of host PKR/eIFalpha signaling / negative stranded viral RNA replication / protein serine/threonine kinase inhibitor activity / symbiont-mediated suppression of host gene expression / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus
Similarity search - Function
Phlebovirus, non structural protein / Rift valley fever virus non structural protein-like / Rift valley fever virus non structural protein (NSs) like
Similarity search - Domain/homology
Non-structural protein S / Non-structural protein S
Similarity search - Component
Biological speciesRift valley fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsBarski, M.S. / Potter, J.A. / Schwarz-Linek, U.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MDTG10 - G1000407/1 United Kingdom
CitationJournal: Elife / Year: 2017
Title: Rift Valley fever phlebovirus NSs protein core domain structure suggests molecular basis for nuclear filaments.
Authors: Barski, M. / Brennan, B. / Miller, O.K. / Potter, J.A. / Vijayakrishnan, S. / Bhella, D. / Naismith, J.H. / Elliott, R.M. / Schwarz-Linek, U.
History
DepositionAug 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-structural protein NS-S
B: Non-structural protein NS-S


Theoretical massNumber of molelcules
Total (without water)38,0992
Polymers38,0992
Non-polymers00
Water1,856103
1
A: Non-structural protein NS-S


Theoretical massNumber of molelcules
Total (without water)19,0491
Polymers19,0491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-structural protein NS-S


Theoretical massNumber of molelcules
Total (without water)19,0491
Polymers19,0491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.500, 124.500, 174.260
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 164
2010B2 - 164

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Components

#1: Protein Non-structural protein NS-S


Mass: 19049.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rift valley fever virus / Gene: NSs / Plasmid: pMAL-C2x / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2SZX2, UniProt: P21698*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.23 Å3/Da / Density % sol: 76.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 10000, NaCl, HEPES, DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 2 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 2.19→107.83 Å / Num. obs: 41684 / % possible obs: 99.9 % / Redundancy: 45 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 32.3
Reflection shellResolution: 2.19→2.25 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
xia2data scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→107.82 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.451 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.125
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 2065 5 %RANDOM
Rwork0.2012 ---
obs0.2019 39005 99.91 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 162.73 Å2 / Biso mean: 63.474 Å2 / Biso min: 31.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.06 Å20 Å2
2--0.13 Å20 Å2
3----0.41 Å2
Refinement stepCycle: final / Resolution: 2.2→107.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 0 103 2597
Biso mean---52.18 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192546
X-RAY DIFFRACTIONr_bond_other_d0.0060.022535
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.9763447
X-RAY DIFFRACTIONr_angle_other_deg1.34435815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9595317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.13122.991107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57315460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0451524
X-RAY DIFFRACTIONr_chiral_restr0.0980.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212803
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02565
Refine LS restraints NCS

Ens-ID: 1 / Number: 18558 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 156 -
Rwork0.395 2817 -
all-2973 -
obs--99.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.41440.3511-0.26471.6415-0.44562.7625-0.0906-0.121-0.06710.07760.1029-0.12850.10060.2719-0.01230.03960.0727-0.01340.3619-0.02750.014116.176-0.949102.106
24.0289-0.7553-0.63244.69031.05732.1664-0.08190.19180.667-0.55930.5615-0.5131-0.37250.5823-0.47960.1503-0.19640.08510.7547-0.11510.525845.28814.00884.134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A79 - 166
2X-RAY DIFFRACTION2B80 - 164

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