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Yorodumi- PDB-3eyf: Crystal structure of anti-human cytomegalovirus antibody 8f9 plus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eyf | ||||||
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Title | Crystal structure of anti-human cytomegalovirus antibody 8f9 plus gB peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / cytomegalovirus / antibody / Immunoglobulin domain / Cleavage on pair of basic residues / Envelope protein / Glycoprotein / Host-virus interaction / Membrane / Transmembrane / Virion | ||||||
Function / homology | Function and homology information host cell Golgi membrane / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Thomson, C.A. / Bryson, S. / McLean, G.R. / Creagh, A.L. / Pai, E.F. / Schrader, J.W. | ||||||
Citation | Journal: Embo J. / Year: 2008 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eyf.cif.gz | 188.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eyf.ent.gz | 148.5 KB | Display | PDB format |
PDBx/mmJSON format | 3eyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/3eyf ftp://data.pdbj.org/pub/pdb/validation_reports/ey/3eyf | HTTPS FTP |
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-Related structure data
Related structure data | 3eyoC 3eyqC 3f12C 1hezS C: citing same article (ref.) 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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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.) Homo sapiens (human) / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6PJF2*PLUS #2: Antibody | Mass: 25932.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET40 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q68CN4*PLUS #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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