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- PDB-1ebo: CRYSTAL STRUCTURE OF THE EBOLA VIRUS MEMBRANE-FUSION SUBUNIT, GP2... -

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Entry
Database: PDB / ID: 1ebo
TitleCRYSTAL STRUCTURE OF THE EBOLA VIRUS MEMBRANE-FUSION SUBUNIT, GP2, FROM THE ENVELOPE GLYCOPROTEIN ECTODOMAIN
ComponentsEBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
KeywordsVIRAL PROTEIN / MEMBRANE FUSION SUBUNIT
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / extracellular region / membrane
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 / Envelope glycoprotein
Similarity search - Component
Biological speciesEbola virus sp.
MethodX-RAY DIFFRACTION / SIR / Resolution: 3 Å
AuthorsWeissenhorn, W. / Carfi, A. / Lee, K.H. / Skehel, J.J. / Wiley, D.C.
CitationJournal: Mol.Cell / Year: 1998
Title: Crystal structure of the Ebola virus membrane fusion subunit, GP2, from the envelope glycoprotein ectodomain.
Authors: Weissenhorn, W. / Carfi, A. / Lee, K.H. / Skehel, J.J. / Wiley, D.C.
History
DepositionNov 3, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 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

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Assembly

Deposited unit
A: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
B: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
C: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
D: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
E: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
F: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,42411
Polymers92,1576
Non-polymers2675
Water00
1
A: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
B: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
C: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1795
Polymers46,0783
Non-polymers1012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12310 Å2
ΔGint-164 kcal/mol
Surface area17290 Å2
MethodPISA
2
D: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
E: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
F: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2456
Polymers46,0783
Non-polymers1663
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12070 Å2
ΔGint-177 kcal/mol
Surface area17150 Å2
MethodPISA
3
D: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
E: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
F: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
hetero molecules

A: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
B: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
C: EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,42411
Polymers92,1576
Non-polymers2675
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556x+1/2,y+1/2,z+11
Buried area24090 Å2
ΔGint-328 kcal/mol
Surface area34480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.702, 32.691, 168.863
Angle α, β, γ (deg.)90.00, 119.23, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein
EBOLA VIRUS ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP2


Mass: 15359.446 Da / Num. of mol.: 6 / Fragment: GCN4 IS RESIDUE 3 - 32, GP2 IS RESIDUE 51 - 133 / Mutation: C55E, C108R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus sp. / Genus: Ebola-like viruses / Production host: Escherichia coli (E. coli)
References: UniProt: Q913A3, GenBank: 4389202, GenBank: 4389203, GenBank: 4389204, GenBank: 4389205, GenBank: 4389206, UniProt: O11457*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
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: 2.24 Å3/Da / Density % sol: 35 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
pH: 9.3 / Method: vapor diffusion, hanging drop
Details: 0.02ml of protein solution was mixed with 0.01ml of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
220 mMTris-HCl1drop
3100 mMTris-HCl1reservoir
430-34 %PEG40001reservoir
5220 mMammonium sulfate1reservoir
61.0 %dioxane1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 17123 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rsym value: 0.083
Reflection shellResolution: 3→3.09 Å / Redundancy: 3.07 % / Rsym value: 0.29 / % possible all: 99.2
Reflection
*PLUS
Num. measured all: 87380 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.29

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
X-PLOR3.851refinement
CCP4phasing
RefinementMethod to determine structure: SIR / Resolution: 3→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: REFINEMENT WAS CONCLUDED USING CNS. A BULK SOLVENT CORRECTION WAS APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.256 -5 %RANDOM
Rwork0.239 ---
obs-87380 99.3 %-
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5326 0 5 0 5331
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.7 Å2

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