[English] 日本語
Yorodumi
- PDB-2ebo: CORE STRUCTURE OF GP2 FROM EBOLA VIRUS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ebo
TitleCORE STRUCTURE OF GP2 FROM EBOLA VIRUS
ComponentsEBOLA VIRUS ENVELOPE GLYCOPROTEIN
KeywordsENVELOPE GLYCOPROTEIN / FILOVIRUS / EBOLA VIRUS / GP2 / COAT PROTEIN
Function / homology
Function and homology information


host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / membrane raft / symbiont entry into host cell / fusion of virus membrane with host endosome membrane ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / membrane raft / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell plasma membrane / virion membrane / extracellular region / identical protein binding
Similarity search - Function
Helix Hairpins - #210 / : / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus - Mayinga (Zaire
1976)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMalashkevich, V.N. / Schneider, B.J. / Mcnally, M.L. / Milhollen, M.A. / Pang, J.X. / Kim, P.S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Core structure of the envelope glycoprotein GP2 from Ebola virus at 1.9-A resolution.
Authors: Malashkevich, V.N. / Schneider, B.J. / McNally, M.L. / Milhollen, M.A. / Pang, J.X. / Kim, P.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystal Structure of the Simian Immunodeficiency Virus (Siv) Gp41 Core: Conserved Helical Interactions Underlie the Broad Inhibitory Activity of Gp41 Peptides
Authors: Malashkevich, V.N. / Chan, D.C. / Chutkowski, C.T. / Kim, P.S.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Core Structure of Gp41 from the HIV Envelope Glycoprotein
Authors: Chan, D.C. / Fass, D. / Berger, J.M. / Kim, P.S.
History
DepositionDec 24, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EBOLA VIRUS ENVELOPE GLYCOPROTEIN
B: EBOLA VIRUS ENVELOPE GLYCOPROTEIN
C: EBOLA VIRUS ENVELOPE GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6704
Polymers25,6343
Non-polymers351
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-87 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.660, 75.660, 67.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.851698, -0.033786, 0.522913), (-0.475861, -0.467666, 0.744878), (0.219383, -0.883265, -0.414393)3.00873, 33.22936, 11.88738
2given(0.851983, -0.476147, 0.217648), (-0.018012, -0.442191, -0.89674), (0.523242, 0.760111, -0.385322)10.61292, 25.3933, -21.71742

-
Components

#1: Protein EBOLA VIRUS ENVELOPE GLYCOPROTEIN


Mass: 8544.757 Da / Num. of mol.: 3 / Fragment: PROTEASE-RESISTANT FRAGMENT / Mutation: C609A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus - Mayinga (Zaire, 1976)
Genus: Ebola-like viruses / Species: Zaire ebolavirus / Strain: Zaire Mayinga / Cellular location: VIRAL MEMBRANE / Gene: GP41 / Variant: ZAIRE ISOLATE / Plasmid: PMMHB / Species (production host): Escherichia coli / Gene (production host): GP41 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q05320
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Description: TRIAL MODEL CONTAINED ONLY 36% OF THE ATOMS OF THE TARGET STRUCTURE.
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
216-18 %isopropanol1reservoir
3100 mMsodium acetate1reservoirpH4.6
4100-200 mM1reservoirCaCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.01
DetectorType: ADSC / Detector: CCD / Date: Dec 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 17326 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 18.8
Reflection shellResolution: 1.9→1.92 Å / Redundancy: 4 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.309 / % possible all: 99.1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. measured all: 86630
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.93 Å / % possible obs: 99.1 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.5refinement
CNS0.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MOF

1mof


Resolution: 1.9→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1363158.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1758 10.2 %RANDOM
Rwork0.205 ---
obs0.205 17303 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 96.68 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 40.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.23 Å20 Å2
2--0.65 Å20 Å2
3----1.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 1 214 2021
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.362.5
X-RAY DIFFRACTIONc_mcangle_it3.213
X-RAY DIFFRACTIONc_scbond_it2.953
X-RAY DIFFRACTIONc_scangle_it4.133.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 283 9.9 %
Rwork0.239 2579 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.269
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
LS refinement shell
*PLUS
Lowest resolution: 1.93 Å / Rfactor obs: 0.239

+
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