[English] 日本語
Yorodumi
- PDB-3vne: Structure of the ebolavirus protein VP24 from Sudan -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vne
TitleStructure of the ebolavirus protein VP24 from Sudan
ComponentsMembrane-associated protein VP24
KeywordsVIRAL PROTEIN / ebolavirus / interferon antagonist / VP24 / STAT1 / Zaire / Sudan / Reston / VP35 / karyopherin alpha / IFN response pathway
Function / homology
Function and homology information


host cell endomembrane system / viral process / symbiont-mediated suppression of host innate immune response / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Filovirus membrane-associated VP24 / Filovirus membrane-associated protein VP24
Similarity search - Domain/homology
Membrane-associated protein VP24 / Membrane-associated protein VP24
Similarity search - Component
Biological speciesSudan ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, A.P.P.
CitationJournal: Plos Pathog. / Year: 2012
Title: The ebola virus interferon antagonist VP24 directly binds STAT1 and has a novel, pyramidal fold
Authors: Zhang, A.P.P. / Bornholdt, Z.A. / Liu, T. / Abelson, D.M. / Lee, D.E. / Li, S. / Woods Jr., V.L. / Saphire, E.O.
History
DepositionJan 12, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Membrane-associated protein VP24


Theoretical massNumber of molelcules
Total (without water)25,3791
Polymers25,3791
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Membrane-associated protein VP24

A: Membrane-associated protein VP24


Theoretical massNumber of molelcules
Total (without water)50,7592
Polymers50,7592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area1760 Å2
ΔGint-13 kcal/mol
Surface area21860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.052, 61.052, 130.352
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-377-

HOH

-
Components

#1: Protein Membrane-associated protein VP24 / Minor matrix protein


Mass: 25379.445 Da / Num. of mol.: 1 / Fragment: UNP residues 9-232 / Mutation: V22A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sudan ebolavirus / Gene: VP24 / Production host: Escherichia coli (E. coli) / References: UniProt: B0LPM0, UniProt: Q5XX02*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES, 0.1M MgCl, 8% PEG 550mme, pH 7.5, vapor diffusion, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2010
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→33.6 Å / Num. all: 19597 / Num. obs: 19519 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 43.62 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.4
Reflection shellHighest resolution: 2 Å / % possible all: 99.6

-
Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→33.569 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7373 / SU ML: 0.38 / σ(F): 0 / Phase error: 31.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2628 1787 9.92 %random
Rwork0.2197 ---
all0.2241 19597 --
obs0.2241 18009 91.5 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.299 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 142.86 Å2 / Biso mean: 53.0937 Å2 / Biso min: 24.27 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→33.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 0 77 1794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151842
X-RAY DIFFRACTIONf_angle_d1.1062408
X-RAY DIFFRACTIONf_chiral_restr0.071286
X-RAY DIFFRACTIONf_plane_restr0.005303
X-RAY DIFFRACTIONf_dihedral_angle_d13.721646
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0001-2.07160.49861480.43791407155581
2.0716-2.15450.40221510.39581443159483
2.1545-2.25250.39751670.34461471163884
2.2525-2.37130.38361680.33771501166987
2.3713-2.51980.35291790.30651658183794
2.5198-2.71430.37661870.26241691187896
2.7143-2.98730.27741940.23681697189197
2.9873-3.41920.26972010.22221752195398
3.4192-4.30630.21521970.17311765196298
4.3063-33.57410.20131950.17481837203296
Refinement TLS params.Method: refined / Origin x: -22.4122 Å / Origin y: -4.6759 Å / Origin z: -4.8694 Å
111213212223313233
T0.3849 Å20.0094 Å2-0.047 Å2-0.2268 Å20.0115 Å2--0.1893 Å2
L1.7535 °20.2729 °2-0.4087 °2-0.8026 °20.0287 °2--1.2472 °2
S0.0752 Å °-0.2275 Å °-0.119 Å °0.1921 Å °-0.0019 Å °0.0138 Å °0.2763 Å °0.1992 Å °-0.0563 Å °
Refinement TLS groupSelection details: (chain A and resid 9:232)

+
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