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- PDB-2ebo: CORE STRUCTURE OF GP2 FROM EBOLA VIRUS -

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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


symbiont-mediated killing of host cell / 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 / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / membrane raft / fusion of virus membrane with host endosome membrane ...symbiont-mediated killing of host cell / 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 / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont entry into host cell / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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 %

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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

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