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- PDB-4zti: Ebola virus nucleoprotein bound to VP35 chaperoning peptide P212121 -

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Basic information

Entry
Database: PDB / ID: 4zti
TitleEbola virus nucleoprotein bound to VP35 chaperoning peptide P212121
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 / symbiont-mediated suppression of host innate immune response / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKirchdoerfer, R.N. / Abelson, D.M. / Saphire, E.O.
Funding support United States, 6items
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
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 P212121
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 / Derived calculations ...Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.version
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase cofactor VP35,Nucleoprotein
B: Polymerase cofactor VP35,Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)84,6252
Polymers84,6252
Non-polymers00
Water4,017223
1
A: Polymerase cofactor VP35,Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)42,3121
Polymers42,3121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polymerase cofactor VP35,Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)42,3121
Polymers42,3121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.881, 94.951, 112.106
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,Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 42312.449 Da / Num. of mol.: 2
Fragment: 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


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.4 / Details: 2.0 M sodium formate, 100 mM sodium acetate pH 4.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03318 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 5, 2014
RadiationMonochromator: Double Si(111) crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.4→48.27 Å / Num. obs: 40325 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.06 / Net I/σ(I): 8.2 / Num. measured all: 298839
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.4-2.497.51.5561.53112941540.5750.60799.8
8.98-48.276.30.09118.655668820.9890.03999.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
Aimless0.1.27data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZTA

4zta


Resolution: 2.4→48.27 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2576 / WRfactor Rwork: 0.1999 / FOM work R set: 0.8139 / SU R Cruickshank DPI: 0.2733 / SU Rfree: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.273 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2050 5.1 %RANDOM
Rwork0.1918 ---
obs0.1946 38215 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 173.25 Å2 / Biso mean: 64.962 Å2 / Biso min: 25.96 Å2
Baniso -1Baniso -2Baniso -3
1--3.25 Å20 Å2-0 Å2
2--1.96 Å20 Å2
3---1.29 Å2
Refinement stepCycle: final / Resolution: 2.4→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5280 0 0 223 5503
Biso mean---60.7 -
Num. residues----673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195381
X-RAY DIFFRACTIONr_bond_other_d00.025282
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9527256
X-RAY DIFFRACTIONr_angle_other_deg3.701312082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4165666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.38824.252254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48215949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.871532
X-RAY DIFFRACTIONr_chiral_restr0.0910.2819
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026113
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021293
X-RAY DIFFRACTIONr_mcbond_it4.3596.0442685
X-RAY DIFFRACTIONr_mcbond_other4.3566.0422684
X-RAY DIFFRACTIONr_mcangle_it6.3399.0313341
LS refinement shellResolution: 2.399→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 148 -
Rwork0.312 2741 -
all-2889 -
obs--99.48 %

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