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- PDB-5bpv: Crystal Structure of Zaire ebolavirus VP35 RNA binding domain mut... -

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Basic information

Entry
Database: PDB / ID: 5bpv
TitleCrystal Structure of Zaire ebolavirus VP35 RNA binding domain mutant I278A
ComponentsPolymerase cofactor VP35
KeywordsVIRAL PROTEIN / Polymerase cofactor / Interferon inhibitor
Function / homology
Function and homology information


suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / molecular sequestering activity / positive regulation of protein sumoylation ...suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / molecular sequestering activity / positive regulation of protein sumoylation / : / viral transcription / viral genome replication / virion component / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / viral nucleocapsid / host cell cytoplasm / negative regulation of gene expression / RNA binding
Similarity search - Function
Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain / Filoviridae VP35, C-terminal inhibitory domain, helical subdomain / Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / Seminal Fluid Protein PDC-109 (Domain B) / Helicase, Ruva Protein; domain 3 ...Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain / Filoviridae VP35, C-terminal inhibitory domain, helical subdomain / Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / Seminal Fluid Protein PDC-109 (Domain B) / Helicase, Ruva Protein; domain 3 / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Polymerase cofactor VP35 / Polymerase cofactor VP35
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.952 Å
AuthorsFadda, V. / Cannas, V. / Zinzula, L. / Distinto, S. / Daino, G.L. / Bianco, G. / Corona, A. / Esposito, F. / Alcaro, S. / Maccioni, E. ...Fadda, V. / Cannas, V. / Zinzula, L. / Distinto, S. / Daino, G.L. / Bianco, G. / Corona, A. / Esposito, F. / Alcaro, S. / Maccioni, E. / Tramontano, E. / Taylor, G.L.
CitationJournal: to be published
Title: Crystal Structure of Zaire ebolavirus VP35 RNA binding domain mutant I278A
Authors: Fadda, V. / Cannas, V. / Zinzula, L. / Distinto, S. / Daino, G.L. / Bianco, G. / Corona, A. / Esposito, F. / Alcaro, S. / Maccioni, E. / Tramontano, E. / Taylor, G.L.
History
DepositionMay 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
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: Polymerase cofactor VP35
B: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)27,3122
Polymers27,3122
Non-polymers00
Water4,738263
1
A: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)13,6561
Polymers13,6561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)13,6561
Polymers13,6561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.750, 65.660, 72.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Polymerase cofactor VP35


Mass: 13655.817 Da / Num. of mol.: 2 / Fragment: RNA binding domain, UNP residues 217-340 / Mutation: I278A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Gene: VP35 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6V1Q9, UniProt: Q05127*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium sodium tartrate tetrahydrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.952→48.522 Å / Num. all: 18397 / Num. obs: 18397 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 13.23 Å2 / Rpim(I) all: 0.043 / Rrim(I) all: 0.113 / Rsym value: 0.104 / Net I/av σ(I): 5.72 / Net I/σ(I): 11.8 / Num. measured all: 122680
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.95-2.065.20.2812.71376026540.1350.2814.899.7
2.06-2.186.80.2183.51702724910.090.2187.2100
2.18-2.336.90.1784.21640523630.0730.1788.4100
2.33-2.5270.1445.11542422080.0590.1449.8100
2.52-2.7670.1215.91425720340.0490.12111.3100
2.76-3.0970.0997.11301018610.040.09913.6100
3.09-3.5670.0738.81154216450.030.07318.7100
3.56-4.366.90.0678.4975214200.0270.06722.1100
4.36-6.176.80.0667.7762611170.0270.06620.1100
6.17-13.9056.40.0636.938776040.0270.06319.391.6

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FKE

3fke


Resolution: 1.952→13.905 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2184 939 5.12 %
Rwork0.1802 17395 -
obs0.1821 18334 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.39 Å2 / Biso mean: 22.7715 Å2 / Biso min: 6.11 Å2
Refinement stepCycle: final / Resolution: 1.952→13.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 0 263 2172
Biso mean---28.02 -
Num. residues----247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071993
X-RAY DIFFRACTIONf_angle_d1.032710
X-RAY DIFFRACTIONf_chiral_restr0.063302
X-RAY DIFFRACTIONf_plane_restr0.004362
X-RAY DIFFRACTIONf_dihedral_angle_d13.403764
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.952-2.05460.28541200.2242456257699
2.0546-2.18290.241530.193924152568100
2.1829-2.35070.21311490.183724362585100
2.3507-2.58590.2291230.187324742597100
2.5859-2.95690.22341300.184624812611100
2.9569-3.71360.20971460.166524972643100
3.7136-13.9050.18361180.163826362754100

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