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Yorodumi- PDB-3ujj: Crystal structure of anti-HIV-1 V3 Fab 4025 in complex with Con A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ujj | ||||||
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Title | Crystal structure of anti-HIV-1 V3 Fab 4025 in complex with Con A peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Ig domains / antibody Fab / antigen binding / The third variable region of HIV-1 gp120 | ||||||
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 / viral process / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / viral process / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kong, X.P. / Sampson, J. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Human Anti-V3 HIV-1 Monoclonal Antibodies Encoded by the VH5-51/VL Lambda Genes Define a Conserved Antigenic Structure. Authors: Gorny, M.K. / Sampson, J. / Li, H. / Jiang, X. / Totrov, M. / Wang, X.H. / Williams, C. / O'Neal, T. / Volsky, B. / Li, L. / Cardozo, T. / Nyambi, P. / 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 | 3ujj.cif.gz | 120.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ujj.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ujj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ujj_validation.pdf.gz | 484.5 KB | Display | wwPDB validaton report |
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Full document | 3ujj_full_validation.pdf.gz | 490.8 KB | Display | |
Data in XML | 3ujj_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 3ujj_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/3ujj ftp://data.pdbj.org/pub/pdb/validation_reports/uj/3ujj | HTTPS FTP |
-Related structure data
Related structure data | 3ujiC 2b0sS C: citing same article (ref.) S: Starting model for refinement |
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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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Details | The Fab is the biological assembly and there is only one Fab in the asymmetric subunit. |
-Components
-Protein/peptide , 1 types, 1 molecules P
#3: Protein/peptide | Mass: 2452.747 Da / Num. of mol.: 1 / Fragment: unp residues 30-52 / Source method: obtained synthetically Details: Synthesized based on HIV-1 strain of consensus clade A Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YXJ8, UniProt: Q9Q714*PLUS |
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-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 22903.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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#2: Antibody | Mass: 24340.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
-Non-polymers , 4 types, 523 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-ACT / #7: 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: 3.95 Å3/Da / Density % sol: 68.86 % |
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Crystal grow | Temperature: 296 K / Method: evaporation / pH: 3.8 Details: 1.6 M ammonium sulfate, 80 mM sodium acetate, 30% glycerol, pH 3.8, EVAPORATION, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97883 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 12, 2009 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97883 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 52860 / Num. obs: 52523 / % possible obs: 91.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rsym value: 0.081 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 67.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 2B0S Resolution: 2→39.301 Å / SU ML: 0.61 / σ(F): 1.35 / Phase error: 19.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.199 Å2 / ksol: 0.382 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→39.301 Å
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Refine LS restraints |
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LS refinement shell |
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