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- PDB-3go1: Crystal structure of anti-HIV-1 Fab 268-D in complex with V3 pept... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3go1 | ||||||
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Title | Crystal structure of anti-HIV-1 Fab 268-D in complex with V3 peptide MN | ||||||
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![]() | IMMUNE SYSTEM / HIV / V3 loop / antibody-antigen interactions / AIDS / Apoptosis / Cell membrane / Cleavage on pair of basic residues / Disulfide bond / Envelope protein / Fusion protein / Glycoprotein / Host-virus interaction / Membrane / Transmembrane / Viral immunoevasion / Virion | ||||||
Function / homology | ![]() Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / 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 ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / 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 / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kong, X.P. / Burke, V.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.9 KB | Display | ![]() |
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PDB format | ![]() | 78.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3mlrC ![]() 3mlsC ![]() 3mltC ![]() 3mluC ![]() 3mlvC ![]() 3mlwC ![]() 3mlxC ![]() 3mlyC ![]() 3mlzC ![]() 1u6aS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 22395.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: B cell / Source: (natural) ![]() | ||
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#2: Antibody | Mass: 23639.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: B cell / Source: (natural) ![]() | ||
#3: Protein/peptide | Mass: 1676.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||
#4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.31 % |
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Crystal grow | Temperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG 8000, 0.2M Ammonium Acetate, 0.1M Sodium Cacodylate pH 6.5, vapor diffusion, hanging drop, temperature 296.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 27, 2008 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→30.6 Å / Num. obs: 34455 / % possible obs: 84.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.212 / Rsym value: 0.212 |
Reflection shell | Resolution: 1.88→1.95 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 0.742 / Rsym value: 0.378 / % possible all: 19.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1U6A Resolution: 1.89→27.1 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.231 / SU ML: 0.097 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 27.104 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.89→27.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.938 Å / Total num. of bins used: 20
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Xplor file |
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