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Yorodumi- PDB-6lsa: Complex structure of bovine herpesvirus 1 glycoprotein D and bovi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lsa | |||||||||
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Title | Complex structure of bovine herpesvirus 1 glycoprotein D and bovine nectin-1 IgV | |||||||||
Components |
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Keywords | VIRAL PROTEIN / complex structure | |||||||||
Function / homology | Function and homology information : / desmosome organization / protein localization to cell junction / lens morphogenesis in camera-type eye / enamel mineralization / cell-cell contact zone / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of synapse assembly / apical junction complex / homophilic cell adhesion via plasma membrane adhesion molecules ...: / desmosome organization / protein localization to cell junction / lens morphogenesis in camera-type eye / enamel mineralization / cell-cell contact zone / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of synapse assembly / apical junction complex / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / hippocampal mossy fiber to CA3 synapse / adherens junction / retina development in camera-type eye / signaling receptor activity / iron ion transport / membrane => GO:0016020 / viral envelope / virion attachment to host cell / protein homodimerization activity Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) Bovine alphaherpesvirus 1 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å | |||||||||
Authors | Yue, D. / Chen, Z.J. / Yang, F.L. / Ye, F. / Lin, S. / Cheng, Y.W. / Wang, J.C. / Chen, Z.M. / Lin, X. / Yang, J. ...Yue, D. / Chen, Z.J. / Yang, F.L. / Ye, F. / Lin, S. / Cheng, Y.W. / Wang, J.C. / Chen, Z.M. / Lin, X. / Yang, J. / Chen, H. / Zhang, Z.L. / You, Y. / Sun, H.L. / Wen, A. / Wang, L.L. / Zheng, Y. / Cao, Y. / Li, Y.H. / Lu, G.W. | |||||||||
Citation | Journal: Sci Adv / Year: 2020 Title: Crystal structure of bovine herpesvirus 1 glycoprotein D bound to nectin-1 reveals the basis for its low-affinity binding to the receptor. Authors: Yue, D. / Chen, Z. / Yang, F. / Ye, F. / Lin, S. / He, B. / Cheng, Y. / Wang, J. / Chen, Z. / Lin, X. / Yang, J. / Chen, H. / Zhang, Z. / You, Y. / Sun, H. / Wen, A. / Wang, L. / Zheng, Y. / ...Authors: Yue, D. / Chen, Z. / Yang, F. / Ye, F. / Lin, S. / He, B. / Cheng, Y. / Wang, J. / Chen, Z. / Lin, X. / Yang, J. / Chen, H. / Zhang, Z. / You, Y. / Sun, H. / Wen, A. / Wang, L. / Zheng, Y. / Cao, Y. / Li, Y. / Lu, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lsa.cif.gz | 306.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lsa.ent.gz | 246.7 KB | Display | PDB format |
PDBx/mmJSON format | 6lsa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/6lsa ftp://data.pdbj.org/pub/pdb/validation_reports/ls/6lsa | HTTPS FTP |
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-Related structure data
Related structure data | 6ls9C 5x5wS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 12100.761 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: NECTIN1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: F1MQJ3 #2: Protein | Mass: 34871.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bovine alphaherpesvirus 1 Gene: US6, gD, AAADCAAH_00066, BLEONNCJ_00068, BLPDLEPH_00067, DCJDKEDG_00068, DILPLKIK_00066, DJCKHMNK_00067, HMKIDIGP_00066, LALCDEHK_00068, NBBNDGNH_00066, NCKHNGOI_00066, NFOBEAPH_00067, OCMKPLLD_ ...Gene: US6, gD, AAADCAAH_00066, BLEONNCJ_00068, BLPDLEPH_00067, DCJDKEDG_00068, DILPLKIK_00066, DJCKHMNK_00067, HMKIDIGP_00066, LALCDEHK_00068, NBBNDGNH_00066, NCKHNGOI_00066, NFOBEAPH_00067, OCMKPLLD_00067, OHMFJBFK_00067 Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q76PF1 #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | #5: Water | ChemComp-HOH / | 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: 3.18 Å3/Da / Density % sol: 61.33 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Sodium HEPES, 15% w/v Polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97892 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 58498 / % possible obs: 98.1 % / Redundancy: 6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.783 / Num. unique obs: 5751 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X5W Resolution: 2.204→45.196 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 163.66 Å2 / Biso mean: 61.8638 Å2 / Biso min: 27.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.204→45.196 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -41.252 Å / Origin y: -31.543 Å / Origin z: 30.269 Å
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Refinement TLS group |
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