+Open data
-Basic information
Entry | Database: PDB / ID: 2ebo | ||||||
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Title | CORE STRUCTURE OF GP2 FROM EBOLA VIRUS | ||||||
Components | EBOLA VIRUS ENVELOPE GLYCOPROTEIN | ||||||
Keywords | ENVELOPE 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 / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / host cell plasma membrane / virion membrane / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Zaire ebolavirus - Mayinga (Zaire 1976) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Malashkevich, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ebo.cif.gz | 57.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ebo.ent.gz | 45.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ebo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ebo_validation.pdf.gz | 372.2 KB | Display | wwPDB validaton report |
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Full document | 2ebo_full_validation.pdf.gz | 377.8 KB | Display | |
Data in XML | 2ebo_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 2ebo_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/2ebo ftp://data.pdbj.org/pub/pdb/validation_reports/eb/2ebo | HTTPS FTP |
-Related structure data
Related structure data | 1mofS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | 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 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % Description: TRIAL MODEL CONTAINED ONLY 36% OF THE ATOMS OF THE TARGET STRUCTURE. | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.6 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.01 |
Detector | Type: ADSC / Detector: CCD / Date: Dec 1, 1998 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.01 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 96.68 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.269 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.93 Å / Rfactor obs: 0.239 |