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- PDB-1q1j: Crystal Structure Analysis of anti-HIV-1 Fab 447-52D in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1q1j | ||||||
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Title | Crystal Structure Analysis of anti-HIV-1 Fab 447-52D in complex with V3 peptide | ||||||
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![]() | IMMUNE SYSTEM / Fab-peptide complex / HIV-1 / gp120 / V3 loop | ||||||
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 / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stanfield, R.L. / Gorny, M.K. / Williams, C. / Zolla-Pazner, S. / Wilson, I.A. | ||||||
![]() | ![]() Title: Structural rationale for the broad neutralization of HIV-1 by human monoclonal antibody 447-52D. Authors: Stanfield, R.L. / Gorny, M.K. / Williams, C. / Zolla-Pazner, S. / Wilson, I.A. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.8 KB | Display | ![]() |
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PDB format | ![]() | 141.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.8 KB | Display | ![]() |
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Full document | ![]() | 479.7 KB | Display | |
Data in XML | ![]() | 33.2 KB | Display | |
Data in CIF | ![]() | 45.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fabS S: Starting model for refinement |
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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: 22684.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: isolated from peripheral blood cells / Source: (natural) ![]() #2: Antibody | Mass: 24763.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: isolated from peripheral blood cells / Source: (natural) ![]() #3: Protein/peptide | Mass: 1827.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs in HIV-1 gp120 / References: UniProt: P05877*PLUS #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.7 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.23M ammonium sulfate, 0.1M sodium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.8 Å / Num. all: 35179 / Num. obs: 35179 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 49.9 Å2 / Rsym value: 0.077 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.5→2.54 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.531 / % possible all: 0.952 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 67571 / Rmerge(I) obs: 0.077 |
Reflection shell | *PLUS % possible obs: 95.2 % / Num. unique obs: 1816 / Num. measured obs: 3553 / Rmerge(I) obs: 0.531 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 8FAB Resolution: 2.5→29.8 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.3505 Å2 / ksol: 0.337844 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.249 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.51 |