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Yorodumi- PDB-4zto: Fab/epitope complex structure of rabbit monoclonal antibody R53 t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zto | |||||||||||||||
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Title | Fab/epitope complex structure of rabbit monoclonal antibody R53 targeting an epitope in HIV-1 gp120 C4 region | |||||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / HIV-1 / Env / C4 / CD4 / monoclonal antibody | |||||||||||||||
Function / homology | Function and homology information Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / 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 / structural molecule activity / virion membrane / membrane Similarity search - Function | |||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) Human immunodeficiency virus 1 | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||||||||
Authors | Pan, R. / Kong, X.-P. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Emerg Microbes Infect / Year: 2015 Title: Structural analysis of a novel rabbit monoclonal antibody R53 targeting an epitope in HIV-1 gp120 C4 region critical for receptor and co-receptor binding. Authors: Pan, R. / Chen, Y. / Vaine, M. / Hu, G. / Wang, S. / Lu, 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 | 4zto.cif.gz | 200.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zto.ent.gz | 156.6 KB | Display | PDB format |
PDBx/mmJSON format | 4zto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zto_validation.pdf.gz | 451.3 KB | Display | wwPDB validaton report |
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Full document | 4zto_full_validation.pdf.gz | 456.1 KB | Display | |
Data in XML | 4zto_validation.xml.gz | 42.5 KB | Display | |
Data in CIF | 4zto_validation.cif.gz | 64.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/4zto ftp://data.pdbj.org/pub/pdb/validation_reports/zt/4zto | HTTPS FTP |
-Related structure data
Related structure data | 4ztpC 4jo1S 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23022.432 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human) #2: Antibody | Mass: 23322.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human) #3: Antibody | Mass: 1660.016 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.41 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 24% polyethylene glycol 6000, 0.1 M citric acid, and 0.02% NaN3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→50 Å / Num. obs: 48392 / % possible obs: 99.1 % / Redundancy: 6.5 % / Rsym value: 0.165 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.26→2.3 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.483 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JO1 Resolution: 2.3→44.143 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.28 / Phase error: 19.61 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→44.143 Å
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Refine LS restraints |
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LS refinement shell |
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