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- PDB-4zta: Ebola virus nucleoprotein bound to VP35 chaperoning peptide I212121 -

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Basic information

Entry
Database: PDB / ID: 4zta
TitleEbola virus nucleoprotein bound to VP35 chaperoning peptide I212121
ComponentsPolymerase cofactor VP35,Nucleoprotein
KeywordsVIRAL PROTEIN / nucleoprotein / chaperone / RNA-bindng
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 / viral RNA genome packaging / 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 / viral RNA genome packaging / positive regulation of protein sumoylation / molecular sequestering activity / : / helical viral capsid / 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 / ribonucleoprotein complex / negative regulation of gene expression / RNA binding
Similarity search - Function
Ebola nucleoprotein / Ebola nucleoprotein / 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.
Similarity search - Domain/homology
Nucleoprotein / Polymerase cofactor VP35
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKirchdoerfer, R.N. / Abelson, D.M. / Saphire, E.O.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R56 AI118016-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5T32 AI007354-25 United States
Burroughs Wellcome Fund United States
Skaggs Institute for Chemical Biology United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ACB-12002 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AGM-12006 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: to be published
Title: Ebola virus nucleoprotein bound to VP35 chaperoning peptide I212121
Authors: Kirchdoerfer, R.N. / Abelson, D.M. / Li, S. / Wood, M.R. / Saphire, E.O.
History
DepositionMay 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.title / _entity_src_gen.pdbx_alt_source_flag ..._citation.title / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 11, 2017Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.number_obs / _reflns_shell.percent_possible_all
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase cofactor VP35,Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)42,3121
Polymers42,3121
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.210, 93.140, 114.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Polymerase cofactor VP35,Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 42312.449 Da / Num. of mol.: 1
Fragment: UNP Q05127 residues 15-59,UNP P18272 residues 33-367,UNP Q05127 residues 15-59,UNP P18272 residues 33-367
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76 / Gene: VP35, NP / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 plysS / References: UniProt: Q05127, UniProt: P18272
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 14

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.7 / Details: 2.2M Sodium formate, 100mM NaOAc pH 4.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.70004 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2014 / Details: 1000 um thick sensor
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.70004 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. obs: 19509 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 172.7 % / Biso Wilson estimate: 67.259 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.144 / Rrim(I) all: 0.145 / Χ2: 1.089 / Net I/σ(I): 27.52 / Num. measured all: 4175583
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.2-2.260.5614.9661192678359435955.013100
2.26-2.320.7194.0491.6254783347234724.077100
2.32-2.390.8743.262.44300574335533553.278100
2.39-2.460.922.5793.32296657326432642.593100
2.46-2.540.9492.0254.36282255320732072.037100
2.54-2.630.9711.4776.14271147308930891.486100
2.63-2.730.9861.18.4273538294629461.106100
2.73-2.840.990.90410.42259369280828080.909100
2.84-2.970.9940.62814.74242358272227220.632100
2.97-3.110.9970.45119.65231043264626460.453100
3.11-3.280.9990.29529.5229562245224520.296100
3.28-3.480.9990.19341.53224165238323830.194100
3.48-3.7210.13353.71199498218421840.134100
3.72-4.0210.10663.28183300205320530.107100
4.02-4.410.08479.35182967189418920.08599.9
4.4-4.9210.07386.11160588170317050.074100
4.92-5.6810.07683.64132780151315130.076100
5.68-6.9610.07187.92118857126512650.072100
6.96-9.8410.056103.1790977100110010.057100
9.8410.055111.4484875375330.05599.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XSCALENovember 3, 2014data scaling
PHENIXdev-1839phasing
PDB_EXTRACT3.15data extraction
XDSNovember 3, 2014data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.4→72.36 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.2067 / FOM work R set: 0.8295 / SU R Cruickshank DPI: 0.3046 / SU Rfree: 0.2208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 976 5 %RANDOM
Rwork0.2035 ---
obs0.205 18533 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 197.4 Å2 / Biso mean: 79.841 Å2 / Biso min: 49.51 Å2
Baniso -1Baniso -2Baniso -3
1-3.95 Å20 Å2-0 Å2
2---3.14 Å20 Å2
3----0.82 Å2
Refinement stepCycle: final / Resolution: 2.4→72.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2674 0 0 107 2781
Biso mean---77.16 -
Num. residues----340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192721
X-RAY DIFFRACTIONr_bond_other_d00.022676
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9533664
X-RAY DIFFRACTIONr_angle_other_deg3.96936121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.6565334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84324.141128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44815485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7531517
X-RAY DIFFRACTIONr_chiral_restr0.0950.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023074
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02653
X-RAY DIFFRACTIONr_mcbond_it4.4817.5871354
X-RAY DIFFRACTIONr_mcbond_other4.2787.581353
X-RAY DIFFRACTIONr_mcangle_it5.27111.2671682
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 71 -
Rwork0.244 1341 -
all-1412 -
obs--99.79 %

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