[English] 日本語
Yorodumi
- PDB-1h2c: Ebola virus matrix protein VP40 N-terminal domain in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h2c
TitleEbola virus matrix protein VP40 N-terminal domain in complex with RNA (High-resolution VP40[55-194] variant).
Components
  • 5'-R(*UP*GP*AP)-3'
  • MATRIX PROTEIN VP40
KeywordsVIRUS/VIRAL PROTEIN / FILOVIRUS / EBOLA VIRUS / MATRIX PROTEIN VP40 / ASSEMBLY / BUDDING / VIRUS-VIRAL PROTEIN complex
Function / homology
Function and homology information


intracellular transport of virus / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / viral budding / host cell late endosome membrane / viral budding via host ESCRT complex / host cell membrane / viral budding from plasma membrane / host cell ...intracellular transport of virus / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / viral budding / host cell late endosome membrane / viral budding via host ESCRT complex / host cell membrane / viral budding from plasma membrane / host cell / structural constituent of virion / ribonucleoprotein complex / membrane raft / virus-mediated perturbation of host defense response / host cell plasma membrane / virion membrane / RNA binding / extracellular region / identical protein binding
Similarity search - Function
Matrix protein VP40, N-terminal domain / 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 / Mainly Beta
Similarity search - Domain/homology
RNA / Matrix protein VP40
Similarity search - Component
Biological speciesEBOLA VIRUS
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsGomis-Ruth, F.X. / Dessen, A. / Bracher, A. / Klenk, H.D. / Weissenhorn, W.
Citation
Journal: Structure / Year: 2003
Title: The Matrix Protein Vp40 from Ebola Virus Octamerizes Into Pore-Like Structures with Specific RNA Binding Properties
Authors: Gomis-Ruth, F.X. / Dessen, A. / Timmins, J. / Bracher, A. / Kolesnikowa, L. / Becker, S. / Klenk, H.D. / Weissenhorn, W.
#1: 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.
History
DepositionAug 5, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MATRIX PROTEIN VP40
R: 5'-R(*UP*GP*AP)-3'


Theoretical massNumber of molelcules
Total (without water)16,2582
Polymers16,2582
Non-polymers00
Water2,846158
1
A: MATRIX PROTEIN VP40
R: 5'-R(*UP*GP*AP)-3'
x 8


Theoretical massNumber of molelcules
Total (without water)130,06616
Polymers130,06616
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation8_556-y,-x,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation2_555-x,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)80.510, 80.510, 46.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
Components on special symmetry positions
IDModelComponents
11A-2088-

HOH

21R-2005-

HOH

DetailsBIOLOGICAL RELEVANT UNIT IS OCTAMERIC ASSOCIATIONOF THE PROTEIN SUBUNITS.

-
Components

#1: Protein MATRIX PROTEIN VP40


Mass: 15322.634 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 55-194
Source method: isolated from a genetically manipulated source
Details: VP40[55-194] VARIANT / Source: (gene. exp.) EBOLA VIRUS / Strain: ZAIRE MAYINGA / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q05128
#2: RNA chain 5'-R(*UP*GP*AP)-3'


Mass: 935.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: MRNA STOP CODON SEQUENCE, BIOCHEMICAL SYNTHESIS BY THE EXPRESSION HOST AND UPTAKE BY THE PROTEIN DURING OVEREXPRESSION
Source: (natural) ESCHERICHIA COLI (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE BIOLOGICALLY RELEVANT OLIGOMER IS A HOMO-OCTAMER AS CREATED BY THE CRYSTALLOGRAPHIC 422 ...THE BIOLOGICALLY RELEVANT OLIGOMER IS A HOMO-OCTAMER AS CREATED BY THE CRYSTALLOGRAPHIC 422 SYMMETRY. VITAL ROLE IN VIRUS ASSEMBLY.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 1 UL OF PROTEIN SOLUTION (10 MG/ML) AND 1 UL OF WELL SOLUTION (100 MM HEPES PH 7.5, 1.5 M NH4H2PO4,15 % MPD). HANGING DROP.
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
2100 mMHEPES1reservoirpH7.5
31.5 M1reservoirNH4H2PO4
415 %MPD1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1.069
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.069 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 167556 / % possible obs: 95.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.1
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 19961 / Num. measured all: 167556
Reflection shell
*PLUS
% possible obs: 78.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 1.6

-
Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.6→40 Å / SU B: 1.419 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.076
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1026 5.1 %RANDOM
Rwork0.164 ---
obs0.165 18914 96 %-
Displacement parametersBiso mean: 11.077 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---0.58 Å20 Å2
3---1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 62 0 158 1187
Refinement
*PLUS
Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.18

+
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://pdbjlvh1.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