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Yorodumi- PDB-3mlw: Crystal structure of anti-HIV-1 V3 Fab 1006-15D in complex with a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mlw | ||||||
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Title | Crystal structure of anti-HIV-1 V3 Fab 1006-15D in complex with an MN V3 peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / human monoclonal antibody / Fab / HIV-1 / gp120 / third variable loop / antibody-antigen interaction | ||||||
Function / homology | Function and homology information Dectin-2 family / 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 ...Dectin-2 family / 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 / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) HIV-1 M:B_MN (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Kong, X.-P. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Conserved structural elements in the V3 crown of HIV-1 gp120. Authors: Jiang, X. / Burke, V. / Totrov, M. / Williams, C. / Cardozo, T. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mlw.cif.gz | 182.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mlw.ent.gz | 150.4 KB | Display | PDB format |
PDBx/mmJSON format | 3mlw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/3mlw ftp://data.pdbj.org/pub/pdb/validation_reports/ml/3mlw | HTTPS FTP |
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-Related structure data
Related structure data | 3go1C 3mlrC 3mlsC 3mltC 3mluC 3mlvC 3mlxC 3mlyC 3mlzC 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
#1: Antibody | Mass: 23035.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) #2: Antibody | Mass: 24574.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) #3: Protein/peptide | Mass: 2711.196 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HIV-1 M:B_MN (virus) / References: UniProt: P05877 #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THE FAB WERE MADE BY ENZYME DIGESTION, THEREFORE THE REAL ENDINGS OF THE CHAINS ...AUTHORS STATE THAT THE FAB WERE MADE BY ENZYME DIGESTION, THEREFORE THE REAL ENDINGS OF THE CHAINS ARE UNKNOWN. | |
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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: 2.84 Å3/Da / Density % sol: 56.71 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, K dihydrogen phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 8, 2007 Details: Bent single Si (111) crystal monochromator (horizontal focusing and deflection) with vertical focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 29061 / % possible obs: 94 % / Rmerge(I) obs: 0.156 / Χ2: 0.825 / Net I/σ(I): 5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→42.27 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.866 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 15.659 / SU ML: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.98 Å2 / Biso mean: 48.043 Å2 / Biso min: 9.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→42.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.771 Å / Total num. of bins used: 20
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