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Yorodumi- PDB-6vbo: Crystal structure of anti-HIV-1 antibody DH813 bound to gp120 V2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vbo | ||||||
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Title | Crystal structure of anti-HIV-1 antibody DH813 bound to gp120 V2 peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / Antibody / GP120 V2 / RV305/RV144 / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex | ||||||
Function / homology | Function and homology information positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.683 Å | ||||||
Authors | Janus, B.M. / Ofek, G. | ||||||
Citation | Journal: JCI Insight / Year: 2020 Title: HIV vaccine delayed boosting increases Env variable region 2-specific antibody effector functions. Authors: Easterhoff, D. / Pollara, J. / Luo, K. / Janus, B. / Gohain, N. / Williams, L.D. / Tay, M.Z. / Monroe, A. / Peachman, K. / Choe, M. / Min, S. / Lusso, P. / Zhang, P. / Go, E.P. / Desaire, H. ...Authors: Easterhoff, D. / Pollara, J. / Luo, K. / Janus, B. / Gohain, N. / Williams, L.D. / Tay, M.Z. / Monroe, A. / Peachman, K. / Choe, M. / Min, S. / Lusso, P. / Zhang, P. / Go, E.P. / Desaire, H. / Bonsignori, M. / Hwang, K.K. / Beck, C. / Kakalis, M. / O'Connell, R.J. / Vasan, S. / Kim, J.H. / Michael, N.L. / Excler, J.L. / Robb, M.L. / Rerks-Ngarm, S. / Kaewkungwal, J. / Pitisuttithum, P. / Nitayaphan, S. / Sinangil, F. / Tartaglia, J. / Phogat, S. / Wiehe, K. / Saunders, K.O. / Montefiori, D.C. / Tomaras, G.D. / Moody, M.A. / Arthos, J. / Rao, M. / Joyce, M.G. / Ofek, G.A. / Ferrari, G. / Haynes, B.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vbo.cif.gz | 183.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vbo.ent.gz | 144.2 KB | Display | PDB format |
PDBx/mmJSON format | 6vbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/6vbo ftp://data.pdbj.org/pub/pdb/validation_reports/vb/6vbo | HTTPS FTP |
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-Related structure data
Related structure data | 6vbpC 6vbqC 1fveS 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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Unit cell |
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-Components
#1: Antibody | Mass: 23957.439 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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#2: Protein | Mass: 23501.447 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#3: Protein/peptide | Mass: 2675.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: I2E6B7 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.86 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% 2-propanol, 15% PEG 8000 and 0.1M imidazole pH 6.5 |
-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: RAYONIX MX300-HS / Detector: CCD / Date: Nov 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→50 Å / Num. obs: 52264 / % possible obs: 93.3 % / Redundancy: 4.1 % / Rpim(I) all: 0.061 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.68→1.72 Å / Mean I/σ(I) obs: 1.76 / Num. unique obs: 3994 / Rpim(I) all: 0.061 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FVE Resolution: 1.683→27.748 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 156.49 Å2 / Biso mean: 33.5968 Å2 / Biso min: 13.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.683→27.748 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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