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Yorodumi- PDB-7s1b: Crystal structure of Epstein-Barr virus glycoproteins gH/gL/gp42-... -
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-Basic information
Entry | Database: PDB / ID: 7s1b | ||||||
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Title | Crystal structure of Epstein-Barr virus glycoproteins gH/gL/gp42-peptide in complex with human neutralizing antibodies 769C2 and 770F7 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody / Fab / gH/gL / Epstein-Barr virus / herpesvirus | ||||||
Function / homology | Function and homology information host cell endosome membrane / host cell Golgi apparatus / carbohydrate binding / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Human gammaherpesvirus 4 (Epstein-Barr virus) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å | ||||||
Authors | Chen, W.-H. / Cohen, J.I. / Kanekiyo, M. / Joyce, M.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Immunity / Year: 2022 Title: Epstein-Barr virus gH/gL has multiple sites of vulnerability for virus neutralization and fusion inhibition. Authors: Chen, W.H. / Kim, J. / Bu, W. / Board, N.L. / Tsybovsky, Y. / Wang, Y. / Hostal, A. / Andrews, S.F. / Gillespie, R.A. / Choe, M. / Stephens, T. / Yang, E.S. / Pegu, A. / Peterson, C.E. / ...Authors: Chen, W.H. / Kim, J. / Bu, W. / Board, N.L. / Tsybovsky, Y. / Wang, Y. / Hostal, A. / Andrews, S.F. / Gillespie, R.A. / Choe, M. / Stephens, T. / Yang, E.S. / Pegu, A. / Peterson, C.E. / Fisher, B.E. / Mascola, J.R. / Pittaluga, S. / McDermott, A.B. / Kanekiyo, M. / Joyce, M.G. / 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 | 7s1b.cif.gz | 617 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s1b.ent.gz | 504.2 KB | Display | PDB format |
PDBx/mmJSON format | 7s1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/7s1b ftp://data.pdbj.org/pub/pdb/validation_reports/s1/7s1b | HTTPS FTP |
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-Related structure data
Related structure data | 7s07C 7s08C 7s0jC 5w0kS S: Starting model for refinement 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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Unit cell |
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-Components
-Envelope glycoprotein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 72838.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human gammaherpesvirus 4 (Epstein-Barr virus) Gene: gH, BXLF2 / Production host: Homo sapiens (human) / References: UniProt: P03231 |
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#2: Protein | Mass: 12503.114 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human gammaherpesvirus 4 (Epstein-Barr virus) Gene: gL, BKRF2 / Production host: Homo sapiens (human) / References: UniProt: P03212 |
-Antibody , 4 types, 4 molecules HLXY
#3: Antibody | Mass: 24626.635 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#4: Antibody | Mass: 23397.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#5: Antibody | Mass: 23840.705 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#6: Antibody | Mass: 22782.020 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Protein/peptide / Sugars , 2 types, 5 molecules C
#7: Protein/peptide | Mass: 3766.208 Da / Num. of mol.: 1 / Fragment: Residues 47-79 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human gammaherpesvirus 4 (Epstein-Barr virus) Gene: BZLF2 / Production host: Homo sapiens (human) / References: UniProt: P0C6Z5 |
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#8: Sugar | ChemComp-NAG / |
-Details
Has ligand of interest | N |
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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: 3.04 Å3/Da / Density % sol: 59.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES pH7.4, 24% PEG3350, 7.5% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 3→71.32 Å / Num. obs: 40453 / % possible obs: 89.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 30.02 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 3→3.1 Å / Num. unique obs: 2692 / CC1/2: 0.77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5W0K Resolution: 3.03→71.32 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 29.64 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.49 Å2 / Biso mean: 46.8968 Å2 / Biso min: 6.21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.03→71.32 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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