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Yorodumi- PDB-3lqa: Crystal structure of clade C gp120 in complex with sCD4 and 21c Fab -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lqa | ||||||
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Title | Crystal structure of clade C gp120 in complex with sCD4 and 21c Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / complex / poly reactivity | ||||||
Function / homology | Function and homology information virus-mediated perturbation of host defense response => GO:0019049 / : / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway ...virus-mediated perturbation of host defense response => GO:0019049 / : / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / positive regulation of kinase activity / regulation of T cell activation / T cell receptor complex / extracellular matrix structural constituent / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / regulation of calcium ion transport / macrophage differentiation / Generation of second messenger molecules / T cell differentiation / PD-1 signaling / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / positive regulation of calcium-mediated signaling / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / protein tyrosine kinase binding / positive regulation of establishment of T cell polarity / positive regulation of interleukin-2 production / T cell activation / host cell endosome membrane / Vpu mediated degradation of CD4 / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of T cell activation / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / Cargo recognition for clathrin-mediated endocytosis / Downstream TCR signaling / virus receptor activity / signaling receptor activity / Clathrin-mediated endocytosis / MHC class II protein complex binding / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell / membrane => GO:0016020 / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / viral protein processing / early endosome / cell adhesion / immune response / positive regulation of protein phosphorylation / membrane raft / fusion of virus membrane with host plasma membrane / endoplasmic reticulum lumen / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / structural molecule activity / virion attachment to host cell / endoplasmic reticulum membrane / protein kinase binding / host cell plasma membrane / virion membrane / positive regulation of DNA-templated transcription / enzyme binding / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) HIV-1 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Diskin, R. / Marcovecchio, P.M. / Bjorkman, P.J. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Structure of a clade C HIV-1 gp120 bound to CD4 and CD4-induced antibody reveals anti-CD4 polyreactivity. Authors: Diskin, R. / Marcovecchio, P.M. / Bjorkman, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lqa.cif.gz | 170.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lqa.ent.gz | 139 KB | Display | PDB format |
PDBx/mmJSON format | 3lqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/3lqa ftp://data.pdbj.org/pub/pdb/validation_reports/lq/3lqa | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21472.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD4 / Plasmid: pACgp67b / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: P01730 |
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#2: Protein | Mass: 36794.566 Da / Num. of mol.: 1 / Mutation: T89I, N226D, T232I, N285T, S329N, T388I, N447D Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 (virus) / Gene: env / Plasmid: pACgp67b / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: Q1PHM6 |
#3: Antibody | Mass: 24619.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 |
#4: Antibody | Mass: 22815.264 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 |
#5: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.07 % Description: The diffraction pattern from the crystals was very anisotropic. There is 80% completeness to 3.4A because the crystals diffracted to only 3.9A in the 'b' direction. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% (w/v) PEG monomethyl ether 2000, 5% (v/v) PEG 200, 0.2 M Trimethylamine N-oxide, 0.1 M Tris-HCl pH 8.5 , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.953 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 23, 2009 Details: Flat mirror, double crystal monochromator, vertical and horizontal focussing mirrors |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→84 Å / Num. obs: 14975 / % possible obs: 79 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rsym value: 0.12 |
Reflection shell | Resolution: 3.4→3.58 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.705 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→84 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Group / σ(F): 0
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Solvent computation | Bsol: 75.543 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 285.47 Å2 / Biso mean: 101.992 Å2 / Biso min: 12.02 Å2
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Refinement step | Cycle: LAST / Resolution: 3.4→84 Å
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Refine LS restraints |
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Xplor file |
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