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- PDB-2y6s: Structure of an Ebolavirus-protective antibody in complex with it... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y6s | ||||||
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Title | Structure of an Ebolavirus-protective antibody in complex with its mucin-domain linear epitope | ||||||
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![]() | IMMUNE SYSTEM/VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX | ||||||
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 / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / host cell plasma membrane / virion membrane / extracellular region / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Olal, D.O. / Kuehne, A. / Lee, J.E. / Bale, S. / Dye, J.M. / Saphire, E.O. | ||||||
![]() | ![]() Title: Structure of an Ebola Virus-Protective Antibody in Complex with its Mucin-Domain Linear Epitope. Authors: Olal, D.O. / Kuehne, A. / Bale, S. / Halfmann, P. / Hashiguchi, T. / Fusco, M.L. / Lee, J.E. / King, L.B. / Kawaoka, Y. / 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 | ![]() | 176.2 KB | Display | ![]() |
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PDB format | ![]() | 140 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.1 KB | Display | ![]() |
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Full document | ![]() | 488.2 KB | Display | |
Data in XML | ![]() | 33.7 KB | Display | |
Data in CIF | ![]() | 45 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dggS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
#1: Antibody | Mass: 23762.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: HYBRIDOMA / Source: (natural) ![]() ![]() #2: Antibody | Mass: 22797.408 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: HYBRIDOMA / Source: (natural) ![]() ![]() #3: Protein/peptide | Mass: 1611.946 Da / Num. of mol.: 2 / Fragment: RESIDUES 477-493 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.1 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.1M BIS-TRIS PROPANE PH6.5, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2010 / Details: MIRRORS | |||||||||
Radiation | Monochromator: SIDE SCATTERING BENT CUBE ROOT I BEAM SINGLE CRYSTAL, ASYMMETRIC CUT 4.965 DEGS Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→50 Å / Num. obs: 46342 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Biso Wilson estimate: 44.75 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.9 | |||||||||
Reflection shell | Resolution: 2.8→50 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2.2 / % possible all: 85.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3DGG Resolution: 2.8→38.122 Å / SU ML: 0.41 / σ(F): 0 / Phase error: 31.64 / Stereochemistry target values: ML / Details: RESIDUES 127-133 ARE DISORDERED
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.94 Å2 / ksol: 0.334 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→38.122 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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