+Open data
-Basic information
Entry | Database: PDB / ID: 1ai1 | ||||||
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Title | HIV-1 V3 LOOP MIMIC | ||||||
Components |
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Keywords | COMPLEX (ANTIBODY/PEPTIDE) / COMPLEX (ANTIBODY-PEPTIDE) / ANTIBODY / CONSTRAINED HIV-1 V3 LOOP PEPTIDE / IMMUNOGLOBULIN / COMPLEX (ANTIBODY-PEPTIDE) complex | ||||||
Function / homology | Function and homology information humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / IgG immunoglobulin complex / Dectin-2 family / immunoglobulin mediated immune response ...humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / IgG immunoglobulin complex / Dectin-2 family / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / B cell differentiation / complement activation, classical pathway / host cell endosome membrane / antigen binding / positive regulation of immune response / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / viral protein processing / defense response to bacterium / fusion of virus membrane with host plasma membrane / external side of 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 / extracellular space / extracellular region / membrane / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Ghiara, J.B. / Wilson, I.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Structure-based design of a constrained peptide mimic of the HIV-1 V3 loop neutralization site. Authors: Ghiara, J.B. / Ferguson, D.C. / Satterthwait, A.C. / Dyson, H.J. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ai1.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ai1.ent.gz | 74.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ai1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/1ai1 ftp://data.pdbj.org/pub/pdb/validation_reports/ai/1ai1 | HTTPS FTP |
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-Related structure data
Related structure data | 1acyS 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: 23675.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: EMBL: AJ272393, UniProt: P01837*PLUS |
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#2: Antibody | Mass: 24208.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: UniProt: P01868 |
#3: Protein/peptide | Mass: 2828.366 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THE PEPTIDE IS NUMBERED ACCORDING TO THE BH10 ISOLATE References: UniProt: P05877 |
Compound details | THE PEPTIDE IS NUMBERED ACCORDING TO THE BH10 ISOLATE SEQUENCE (L.RATNER ET AL., NATURE 313:277-284 (1985)). |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.16 Å3/Da / Density % sol: 70.4 % | |||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, sitting drop / PH range low: 6.75 / PH range high: 5 | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.8 Å / Num. obs: 19192 / % possible obs: 92 % / Rsym value: 0.08 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 90 |
Reflection | *PLUS Num. measured all: 50028 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 90 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ACY Resolution: 2.8→12 Å / σ(F): 0
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Displacement parameters | Biso mean: 30 Å2 | |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→12 Å
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||
Refine LS restraints | *PLUS
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