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Yorodumi- PDB-3d0v: Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Anti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d0v | ||||||
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Title | Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 in complex with gp41 Peptide LLELDKWASLW | ||||||
Components |
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Keywords | IMMUNE SYSTEM / 2F5 / HIV / gp41 / antibody / neutralizing | ||||||
Function / homology | Function and homology information virus-mediated perturbation of host defense response => GO:0019049 / : / Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / immunoglobulin complex / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering ...virus-mediated perturbation of host defense response => GO:0019049 / : / Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / immunoglobulin complex / 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 / virus-mediated perturbation of host defense response / 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 / membrane => GO:0016020 / viral protein processing / symbiont entry into host cell / 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 / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Bryson, S. / Julien, J.P. / Pai, E.F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural details of HIV-1 recognition by the broadly neutralizing monoclonal antibody 2F5: epitope conformation, antigen-recognition loop mobility, and anion-binding site. Authors: Julien, J.P. / Bryson, S. / Nieva, J.L. / Pai, E.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d0v.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d0v.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 3d0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/3d0v ftp://data.pdbj.org/pub/pdb/validation_reports/d0/3d0v | HTTPS FTP |
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-Related structure data
Related structure data | 2p8lC 2p8mC 2p8pC 2pr4C 3d0lC 3droC 3drqC 2f5bS 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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-Components
#1: Antibody | Mass: 23363.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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#2: Antibody | Mass: 25245.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NF17*PLUS |
#3: Protein/peptide | Mass: 1374.603 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in the human immunodeficiency virus References: UniProt: Q7SVL4, UniProt: P04578*PLUS |
#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: 3.34 Å3/Da / Density % sol: 63.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M sodium acetate, pH 5.6, 20% 2-propanol, 16-20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 7, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→20 Å / Num. all: 44152 / Num. obs: 42170 / % possible obs: 95.5 % / Biso Wilson estimate: 25.7 Å2 / Rsym value: 0.058 |
Reflection shell | Resolution: 2.05→2.18 Å / Num. unique all: 6083 / Rsym value: 0.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2F5B Resolution: 2.05→19.76 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 965007.6 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.7935 Å2 / ksol: 0.406975 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→19.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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