[English] 日本語
Yorodumi
- PDB-4ztg: Ebola virus nucleoprotein bound to VP35 chaperoning peptide P22121 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ztg
TitleEbola virus nucleoprotein bound to VP35 chaperoning peptide P22121
ComponentsPolymerase cofactor VP35,Nucleoprotein fusion protein
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 / molecular sequestering activity ...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 / molecular sequestering activity / positive regulation of protein sumoylation / : / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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 P22121
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 / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
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_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polymerase cofactor VP35,Nucleoprotein fusion protein


Theoretical massNumber of molelcules
Total (without water)42,3121
Polymers42,3121
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.349, 92.398, 133.626
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

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


Mass: 42312.449 Da / Num. of mol.: 1
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 / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.44 % / Description: Plates
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 12% PEG 6000, 100 mM MES pH 5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 26, 2014 / Details: 1000 um thick sensor
RadiationMonochromator: Double Si(111) crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.8→46.2 Å / Num. obs: 10825 / % possible obs: 99.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 79.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.036 / Net I/σ(I): 12.9 / Num. measured all: 68091
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.8-2.956.21.0421.6926814860.8110.44998.4
8.84-46.25.20.03339.621324100.9990.01599

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
XDSdata scaling
PHASER2.5.7phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→45 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.2759 / WRfactor Rwork: 0.2415 / FOM work R set: 0.7056 / SU Rfree: 0.4449 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.445 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2933 1078 10 %RANDOM
Rwork0.2592 ---
obs0.2625 9707 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.26 Å2 / Biso mean: 90.816 Å2 / Biso min: 42.51 Å2
Baniso -1Baniso -2Baniso -3
1--4.42 Å2-0 Å20 Å2
2--8.12 Å2-0 Å2
3----3.7 Å2
Refinement stepCycle: final / Resolution: 2.8→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2640 0 0 17 2657
Biso mean---61.58 -
Num. residues----338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192687
X-RAY DIFFRACTIONr_bond_other_d00.022662
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9573623
X-RAY DIFFRACTIONr_angle_other_deg4.09636093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.7145334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.70124.228123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5915478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.31516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023043
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02635
X-RAY DIFFRACTIONr_mcbond_it4.1448.7541348
X-RAY DIFFRACTIONr_mcbond_other3.9218.7481347
X-RAY DIFFRACTIONr_mcangle_it4.74713.0421678
LS refinement shellResolution: 2.797→2.869 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 59 -
Rwork0.392 663 -
all-722 -
obs--96.52 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more