[English] 日本語
Yorodumi
- PDB-4or8: Crystal structure of Marburg virus VP24 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4or8
TitleCrystal structure of Marburg virus VP24
ComponentsMembrane-associated protein VP24
KeywordsVIRAL PROTEIN / Marburg / VP24 / pyramidal fold / protein / Ebola / virus / viral
Function / homology
Function and homology information


host cell endomembrane system / viral process / viral nucleocapsid / structural constituent of virion / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Filovirus membrane-associated VP24 / Filovirus membrane-associated protein VP24
Similarity search - Domain/homology
Membrane-associated protein VP24
Similarity search - Component
Biological speciesMarburg virus - Musoke
Kenya
1980
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.654 Å
AuthorsZhang, A.P.P. / Bornholdt, Z. / Abelson, D. / Saphire, E.O.
CitationJournal: J.Virol. / Year: 2014
Title: Crystal Structure of Marburg Virus VP24.
Authors: Zhang, A.P. / Bornholdt, Z.A. / Abelson, D.M. / Saphire, E.O.
History
DepositionFeb 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Feb 28, 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
B: Membrane-associated protein VP24


Theoretical massNumber of molelcules
Total (without water)60,7742
Polymers60,7742
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-30 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.221, 48.078, 64.051
Angle α, β, γ (deg.)88.44, 78.68, 71.34
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Membrane-associated protein VP24


Mass: 30387.223 Da / Num. of mol.: 2 / Fragment: VP24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marburg virus - Musoke, Kenya, 1980 / Strain: Musoke-80 / Gene: VP24 / Production host: Escherichia coli (E. coli) / References: UniProt: P35256
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.99 Å3/Da / Density % sol: 38.07 %
Crystal growTemperature: 273 K / Method: liquid diffusion / pH: 6.5
Details: 0.1M ADA (Hampton Research), 0.1M lithium acetate, 20% glycerol, 2% (v/v) PEG 400 and 8% (v/v) PEG 4000 , pH 6.5, LIQUID DIFFUSION, temperature 273K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2012
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.654→40 Å / Num. all: 13515 / Num. obs: 13245 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.77

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.654→39.209 Å / SU ML: 0.35 / σ(F): 2.04 / Phase error: 26.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 650 4.91 %RANDOM
Rwork0.1798 ---
obs0.1834 13245 98.07 %-
all-13245 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.654→39.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3597 0 0 47 3644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033727
X-RAY DIFFRACTIONf_angle_d0.6165061
X-RAY DIFFRACTIONf_dihedral_angle_d11.7691363
X-RAY DIFFRACTIONf_chiral_restr0.041589
X-RAY DIFFRACTIONf_plane_restr0.003631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6542-2.85910.30341350.21972439X-RAY DIFFRACTION96
2.8591-3.14670.3151330.20862522X-RAY DIFFRACTION98
3.1467-3.60180.24111200.19082539X-RAY DIFFRACTION99
3.6018-4.53680.25091310.16072558X-RAY DIFFRACTION99
4.5368-39.21320.23161310.17112537X-RAY DIFFRACTION99

+
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