[English] 日本語
Yorodumi
- PDB-5toh: Crystal Structure of the Marburg Virus VP35 Oligomerization Domain I2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5toh
TitleCrystal Structure of the Marburg Virus VP35 Oligomerization Domain I2
ComponentsPolymerase cofactor VP35
KeywordsVIRAL PROTEIN / polymerase cofactor / coiled coil / oligomerization / trimer
Function / homologyFiloviruses 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. / viral nucleocapsid / host cell cytoplasm / Polymerase cofactor VP35
Function and homology information
Biological speciesLake Victoria marburgvirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.01 Å
AuthorsBruhn, J.F. / Kirchdoerfer, R.N. / Tickle, I.J. / Bricogne, G. / Saphire, E.O.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32 AI007606 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI118016 United States
Burroughs Wellcome FundInvestigators in the Pathogenesis of Infectious Disease Award 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: J. Virol. / Year: 2017
Title: Crystal Structure of the Marburg Virus VP35 Oligomerization Domain.
Authors: Bruhn, J.F. / Kirchdoerfer, R.N. / Urata, S.M. / Li, S. / Tickle, I.J. / Bricogne, G. / Saphire, E.O.
History
DepositionOct 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Structure summary
Revision 1.2Nov 30, 2016Group: Database references
Revision 1.3Jan 11, 2017Group: Database references
Revision 1.4Feb 8, 2017Group: Database references
Revision 1.5Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Mar 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
B: Polymerase cofactor VP35
C: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)24,6173
Polymers24,6173
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-50 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.690, 35.000, 105.240
Angle α, β, γ (deg.)90.000, 105.280, 90.000
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein Polymerase cofactor VP35


Mass: 8205.597 Da / Num. of mol.: 3 / Fragment: UNP residues 60-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lake Victoria marburgvirus (strain Musoke-80)
Strain: Musoke-80 / Gene: VP35 / Production host: Escherichia coli (E. coli) / References: UniProt: P35259
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Sodium cacodylate pH 6.5, 100 mM Mg-acetate and 18% 2-methyl-2,4-pentanediol (MPD), cryo-protected by addition of 25% ethylene glycol

-
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 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.01→53.02 Å / Num. obs: 7658 / % possible obs: 42.1 % / Redundancy: 2.2 % / Biso Wilson estimate: 41.6 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.139 / Net I/σ(I): 8.3
Reflection shellResolution: 2.01→2.12 Å / Redundancy: 2.1 % / Rmerge(I) obs: 1.009 / Mean I/σ(I) obs: 1 / CC1/2: 0.783 / % possible all: 2.4

-
Processing

Software
NameVersionClassification
PDB_EXTRACT3.2data extraction
Aimlessdata scaling
XDSdata reduction
MR-Rosettaphasing
STARANISOdata scaling
BUSTER2.11.7refinement
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.01→53.02 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.897 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.54 / SU Rfree Blow DPI: 0.302
RfactorNum. reflection% reflectionSelection details
Rfree0.266 377 4.92 %RANDOM
Rwork0.239 ---
obs0.241 7657 42.3 %-
Displacement parametersBiso max: 136.24 Å2 / Biso mean: 45.76 Å2 / Biso min: 15.13 Å2
Baniso -1Baniso -2Baniso -3
1-4.1665 Å20 Å21.2492 Å2
2---1.506 Å20 Å2
3----2.6605 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: final / Resolution: 2.01→53.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1417 0 0 26 1443
Biso mean---39.68 -
Num. residues----175
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d685SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes41HARMONIC2
X-RAY DIFFRACTIONt_gen_planes412HARMONIC5
X-RAY DIFFRACTIONt_it2920HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion215SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3007SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2920HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg5328HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion4.46
X-RAY DIFFRACTIONt_other_torsion15.13
LS refinement shellResolution: 2.01→2.25 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.238 9 4.35 %
Rwork0.24 198 -
all-207 -
obs--4.06 %

+
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