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- PDB-4ijf: Crystal structure of the Zaire ebolavirus VP35 interferon inhibit... -

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Basic information

Entry
Database: PDB / ID: 4ijf
TitleCrystal structure of the Zaire ebolavirus VP35 interferon inhibitory domain K222A/R225A/K248A/K251A mutant
ComponentsPolymerase cofactor VP35
KeywordsVIRAL PROTEIN / IFN inhibition / polymerase cofactor / RNA binding protein / interferon antagonism / dsRNA / virus
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 / : / 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 / : / positive regulation of protein sumoylation / molecular sequestering activity / viral transcription / viral genome replication / 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
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.506 Å
AuthorsBinning, J.B. / Wang, T. / Leung, D.W. / Xu, W. / Borek, D. / Amarasinghe, G.K.
CitationJournal: Biochemistry / Year: 2013
Title: Development of RNA Aptamers Targeting Ebola Virus VP35.
Authors: Binning, J.M. / Wang, T. / Luthra, P. / Shabman, R.S. / Borek, D.M. / Liu, G. / Xu, W. / Leung, D.W. / Basler, C.F. / Amarasinghe, G.K.
History
DepositionDec 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)13,8531
Polymers13,8531
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.704, 59.704, 67.754
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Polymerase cofactor VP35


Mass: 13852.986 Da / Num. of mol.: 1
Fragment: interferon inhibitory domain (UNP residues 218-340)
Mutation: K222A, R225A, K248A, K251A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Strain: Mayinga-76 / Gene: VP35 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05127
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5, 30% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793378 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2011
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793378 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 5063 / % possible obs: 99.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.074 / Χ2: 0.868 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.543.90.772260.9991100
2.54-2.5940.6012740.6821100
2.59-2.644.10.5332350.7831100
2.64-2.6940.4812440.9931100
2.69-2.754.10.3452520.7641100
2.75-2.824.20.3012560.8551100
2.82-2.894.10.2462430.8551100
2.89-2.964.10.2012520.9461100
2.96-3.054.10.1622480.8151100
3.05-3.154.10.1282560.871100
3.15-3.2640.1212511.0111100
3.26-3.394.10.0992410.8691100
3.39-3.5540.0832580.964199.2
3.55-3.7340.0842671.0451100
3.73-3.9740.072531.016199.6
3.97-4.273.90.0622620.911199.6
4.27-4.73.90.0592460.829198.4
4.7-5.383.90.062610.888199.2
5.38-6.783.80.052670.693199.3
6.78-503.50.0442710.564191.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FKE

3fke


Resolution: 2.506→41.104 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7685 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 209 4.52 %RANDOM
Rwork0.2001 ---
obs0.2026 4629 91.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.99 Å2 / Biso mean: 50.2847 Å2 / Biso min: 16.93 Å2
Refinement stepCycle: LAST / Resolution: 2.506→41.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms937 0 0 8 945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01959
X-RAY DIFFRACTIONf_angle_d1.241304
X-RAY DIFFRACTIONf_chiral_restr0.073149
X-RAY DIFFRACTIONf_plane_restr0.006173
X-RAY DIFFRACTIONf_dihedral_angle_d13.856356
LS refinement shellResolution: 2.506→41.1091 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2543 209 -
Rwork0.2001 4420 -
all-4629 -
obs--91 %
Refinement TLS params.Method: refined / Origin x: 26.6011 Å / Origin y: -24.9494 Å / Origin z: 15.0614 Å
111213212223313233
T0.1503 Å2-0.054 Å20.0485 Å2-0.275 Å2-0.0013 Å2--0.2299 Å2
L6.3307 °20.1827 °2-0.5811 °2-2.8213 °20.9573 °2--5.5997 °2
S-0.4219 Å °0.1885 Å °-0.4427 Å °0.0759 Å °-0.0359 Å °0.1192 Å °-0.0571 Å °0.1609 Å °0.1705 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA218 - 340
2X-RAY DIFFRACTION1allA1 - 408

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