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- PDB-3eyf: Crystal structure of anti-human cytomegalovirus antibody 8f9 plus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3eyf | ||||||
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Title | Crystal structure of anti-human cytomegalovirus antibody 8f9 plus gB peptide | ||||||
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![]() | IMMUNE SYSTEM / cytomegalovirus / antibody / Immunoglobulin domain / Cleavage on pair of basic residues / Envelope protein / Glycoprotein / Host-virus interaction / Membrane / Transmembrane / Virion | ||||||
Function / homology | ![]() host cell Golgi membrane / host cell endosome membrane / symbiont entry into host cell / immune response / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular space / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thomson, C.A. / Bryson, S. / McLean, G.R. / Creagh, A.L. / Pai, E.F. / Schrader, J.W. | ||||||
![]() | ![]() Title: Germline V-genes sculpt the binding site of a family of antibodies neutralizing human cytomegalovirus. Authors: Thomson, C.A. / Bryson, S. / McLean, G.R. / Creagh, A.L. / Pai, E.F. / Schrader, J.W. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.3 KB | Display | ![]() |
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PDB format | ![]() | 148.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 491.5 KB | Display | ![]() |
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Full document | ![]() | 513.4 KB | Display | |
Data in XML | ![]() | 38.7 KB | Display | |
Data in CIF | ![]() | 55.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3eyoC ![]() 3eyqC ![]() 3f12C ![]() 1hezS 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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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23714.580 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 25932.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein/peptide | Mass: 1244.394 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Synthetic peptide following the sequence of residues 69-78 of Glycoprotein B from Human cytomegalovirus, UniProt entry P13201 (VGLB_HCMVT) References: UniProt: P13201 #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.86 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.6 Details: 1.9M Ammonium sulfate, 0.1M CAPS buffer, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 12, 2005 |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 42862 / Num. obs: 42862 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 4.5 / % possible all: 95.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1HEZ Resolution: 2.3→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 36.8 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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