[English] 日本語
Yorodumi
- PDB-1es6: CRYSTAL STRUCTURE OF THE MATRIX PROTEIN OF EBOLA VIRUS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1es6
TitleCRYSTAL STRUCTURE OF THE MATRIX PROTEIN OF EBOLA VIRUS
ComponentsMATRIX PROTEIN VP40
KeywordsVIRAL PROTEIN / beta sandwich / anti-parallel strands / beta sheet / helix
Function / homology
Function and homology information


host cell endomembrane system / host cell late endosome membrane / viral budding via host ESCRT complex / structural constituent of virion / symbiont-mediated suppression of host innate immune response / ribonucleoprotein complex / host cell plasma membrane / virion membrane / RNA binding / extracellular region / membrane
Similarity search - Function
EV matrix protein / Matrix protein VP40, N-terminal domain / EV matrix protein fold / EV matrix protein, C-terminal / EV matrix protein / EV matrix domain superfamily / EV matrix protein, N-terminal / Matrix protein VP40 / Topoisomerase I; domain 3 / Distorted Sandwich ...EV matrix protein / Matrix protein VP40, N-terminal domain / EV matrix protein fold / EV matrix protein, C-terminal / EV matrix protein / EV matrix domain superfamily / EV matrix protein, N-terminal / Matrix protein VP40 / Topoisomerase I; domain 3 / Distorted Sandwich / Sandwich / Mainly Beta
Similarity search - Domain/homology
Matrix protein VP40 / Matrix protein VP40
Similarity search - Component
Biological speciesEbola virus sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsDessen, A. / Volchkov, V. / Dolnik, O. / Klenk, H.-D. / Weissenhorn, W.
Citation
Journal: EMBO J. / Year: 2000
Title: Crystal structure of the matrix protein VP40 from Ebola virus.
Authors: Dessen, A. / Volchkov, V. / Dolnik, O. / Klenk, H.D. / Weissenhorn, W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray analysis of the matrix protein from Ebola virus
Authors: Dessen, A. / Forest, E. / Volchkov, V. / Dolnik, O. / Klenk, H.-D. / Weissenhorn, W.
History
DepositionApr 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MATRIX PROTEIN VP40


Theoretical massNumber of molelcules
Total (without water)31,8611
Polymers31,8611
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.637, 91.094, 49.226
Angle α, β, γ (deg.)90.00, 97.35, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein MATRIX PROTEIN VP40


Mass: 31860.824 Da / Num. of mol.: 1 / Mutation: H269L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus sp. / Genus: Ebola-like viruses / Strain: ZAIRE / Description: EBOLA VIRUS RNA GENOME / Plasmid: PRSET / Production host: Escherichia coli (E. coli) / References: UniProt: Q913A4, UniProt: Q77DJ6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris, PEG 750 monomethylether, magnesium chloride, beta-octylglucoside , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: Dessen, A., (2000) Acta Crystallogr., Sect.D, 56, 758.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMTris1reservoir
225 %PEG750 MME1reservoir
3100 mM1reservoirMgCl2
40.2 %beta-octylglucoside1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8855
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8855 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 19062 / Num. obs: 17806 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 24.59 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 10.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.224 / Num. unique all: 1170 / % possible all: 86.6
Reflection
*PLUS
Num. measured all: 166358
Reflection shell
*PLUS
% possible obs: 86.8 % / Mean I/σ(I) obs: 3.8

-
Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1857 10 %RANDOM
Rwork0.22 ---
all0.223 18864 --
obs0.223 17007 98.6 %-
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1965 0 0 121 2086
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.47
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.22 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.3 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.337 / Rfactor obs: 0.278

+
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