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- PDB-6ea7: Structure of EBOV GPcl in complex with the pan-ebolavirus mAb ADI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ea7 | |||||||||
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Title | Structure of EBOV GPcl in complex with the pan-ebolavirus mAb ADI-15878 | |||||||||
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![]() | VIRAL PROTEIN/immune system / mAb / GP / glycoprotein / Ebola / EBOV / antibody / BDBV / bundibugyo / neutralization / immune / bnAb / complex / filovirus / VIRAL PROTEIN / VIRAL PROTEIN-immune system complex | |||||||||
Function / homology | ![]() 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 / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | West, B.R. / Moyer, C.L. / King, L.B. / Fusco, M.L. / Milligan, J.C. / Hui, S. / Saphire, E.O. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis of Pan-Ebolavirus Neutralization by a Human Antibody against a Conserved, yet Cryptic Epitope. Authors: West, B.R. / Moyer, C.L. / King, L.B. / Fusco, M.L. / Milligan, J.C. / Hui, S. / 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 | ![]() | 410 KB | Display | ![]() |
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PDB format | ![]() | 334.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 44.4 KB | Display | |
Data in CIF | ![]() | 64.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ea5C ![]() 5hj3S C: citing same article ( 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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Unit cell |
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Components
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 17778.197 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 12352.092 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Antibody , 2 types, 6 molecules HMQLNR
#3: Antibody | Mass: 24743.570 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Antibody | Mass: 23093.479 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 4 types, 6 molecules ![](data/chem/img/NAG.gif)
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
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#6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Sugar | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.59 Å3/Da / Density % sol: 65.73 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 100 mM MgCl2, 100 mM HEPES pH 7.5, and 10% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4.25→56.08 Å / Num. obs: 24218 / % possible obs: 99.9 % / Redundancy: 173.1 % / Biso Wilson estimate: 133 Å2 / CC1/2: 1 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 4.25→4.4 Å / Redundancy: 162.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4317 / CC1/2: 0.56 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5HJ3 Resolution: 4.25→56.08 Å / SU ML: 0.78 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 34.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.25→56.08 Å
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Refine LS restraints |
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LS refinement shell |
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