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Yorodumi- PDB-8too: Crystal structure of Epstein-Barr virus gp42 in complex with anti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8too | ||||||
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Title | Crystal structure of Epstein-Barr virus gp42 in complex with antibody 4C12 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Viral Protein / Antibody | ||||||
Function / homology | C-type lectin-like/link domain superfamily / C-type lectin fold / host cell membrane / carbohydrate binding / virion membrane / membrane / Glycoprotein 42 Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Epstein-Barr virus (Epstein-Barr virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Bu, W. / Kumar, A. / Board, N. / Kim, J. / Dowdell, K. / Zhang, S. / Lei, Y. / Hostal, A. / Krogmann, T. / Wang, Y. ...Bu, W. / Kumar, A. / Board, N. / Kim, J. / Dowdell, K. / Zhang, S. / Lei, Y. / Hostal, A. / Krogmann, T. / Wang, Y. / Pittaluga, S. / Marcotrigiano, J. / Cohen, J.I. | ||||||
Funding support | United States, 1items
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Citation | Journal: Immunity / Year: 2024 Title: Epstein-Barr virus gp42 antibodies reveal sites of vulnerability for receptor binding and fusion to B cells. Authors: Bu, W. / Kumar, A. / Board, N.L. / Kim, J. / Dowdell, K. / Zhang, S. / Lei, Y. / Hostal, A. / Krogmann, T. / Wang, Y. / Pittaluga, S. / Marcotrigiano, J. / Cohen, J.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8too.cif.gz | 833 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8too.ent.gz | 687.7 KB | Display | PDB format |
PDBx/mmJSON format | 8too.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8too_validation.pdf.gz | 517.2 KB | Display | wwPDB validaton report |
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Full document | 8too_full_validation.pdf.gz | 550 KB | Display | |
Data in XML | 8too_validation.xml.gz | 77.1 KB | Display | |
Data in CIF | 8too_validation.cif.gz | 105 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/8too ftp://data.pdbj.org/pub/pdb/validation_reports/to/8too | HTTPS FTP |
-Related structure data
Related structure data | 8tnnC 8tntC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23604.100 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) #2: Antibody | Mass: 25154.045 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) #3: Protein | Mass: 15946.102 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Epstein-Barr virus (Epstein-Barr virus) Gene: BZLF2 / Production host: Homo sapiens (human) / References: UniProt: P03205 #4: 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: 2.61 Å3/Da / Density % sol: 52.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20mM Tris pH7.5, 150mM NaCl, 0.2M zinc acetate dihydrate, and 18% PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→66.42 Å / Num. obs: 73888 / % possible obs: 91.8 % / Redundancy: 3.8 % / Rsym value: 0.157 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.6→2.6 Å / Num. unique obs: 7047 / Rsym value: 1.187 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→53.51 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→53.51 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 4.1318 Å / Origin y: -18.8885 Å / Origin z: 8.2062 Å
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Refinement TLS group | Selection details: all |