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- PDB-3ve0: Crystal structure of Sudan Ebolavirus Glycoprotein (strain Bonifa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ve0 | |||||||||
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Title | Crystal structure of Sudan Ebolavirus Glycoprotein (strain Boniface) bound to 16F6 | |||||||||
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Function / homology | ![]() clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / entry receptor-mediated virion attachment to host cell / membrane => GO:0016020 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / fusion of virus membrane with host endosome membrane / ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Saphire, E.O. / Bale, S. / Dias, J.M. | |||||||||
![]() | ![]() Title: Structural basis for differential neutralization of ebolaviruses. Authors: Bale, S. / Dias, J.M. / Fusco, M.L. / Hashiguchi, T. / Wong, A.C. / Liu, T. / Keuhne, A.I. / Li, S. / Woods, V.L. / Chandran, K. / Dye, J.M. / Saphire, E.O. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 323.4 KB | Display | ![]() |
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PDB format | ![]() | 263.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3csyS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33404.312 Da / Num. of mol.: 1 / Fragment: Sudan Boniface Glycoprotein Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 18749.258 Da / Num. of mol.: 1 / Fragment: 16F6 chain A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Antibody | Mass: 23686.604 Da / Num. of mol.: 1 / Fragment: 16F6 chain B / Source method: isolated from a natural source Details: Antibody raised by injecting mice with irradiated virus Source: (natural) ![]() ![]() ![]() |
#4: Antibody | Mass: 23457.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Antibody raised by injecting mice with irradiated virus Source: (natural) ![]() ![]() ![]() |
#5: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.38 % |
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Crystal grow![]() | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 15% (w/v) PEG 3350, 0.2 M lithium citrate, and 1.5% benzamidine hydrochloride, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2008 |
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.35→50 Å / Num. all: 17818 / Num. obs: 17818 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.4 % / Rmerge(I) obs: 0.049 / Rsym value: 0.079 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 3.35→3.47 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.777 / % possible all: 100 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3CSY Resolution: 3.353→45.93 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.905 / SU B: 71.763 / SU ML: 0.524 / Cross valid method: THROUGHOUT / ESU R Free: 0.59 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 142.918 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.353→45.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.353→3.439 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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