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Yorodumi- PDB-1g9m: HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND IN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g9m | |||||||||
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Title | HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B | |||||||||
Components |
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Keywords | Viral protein/Immune system / COMPLEX (HIV ENVELOPE PROTEIN-CD4-FAB) / HIV-1 EXTERIOR ENVELOPE GP120 FROM LABORATORY-ADAPTED ISOLATE / HXBC2 / SURFACE T-CELL GLYCOPROTEIN CD4 / ANTIGEN-BINDING FRAGMENT OF HUMAN IMMUNOGLOBULIN 17B / Viral protein-Immune system COMPLEX | |||||||||
Function / homology | Function and homology information helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / Synthesis and processing of ENV and VPU / MHC class II protein binding / evasion of host immune response / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / Synthesis and processing of ENV and VPU / MHC class II protein binding / evasion of host immune response / 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 / Dectin-2 family / 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 / virus-mediated perturbation of host defense response / T cell activation / host cell endosome membrane / actin filament organization / Vpu mediated degradation of CD4 / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / Assembly Of The HIV Virion / Budding and maturation of HIV virion / 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 / 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 / symbiont entry into host cell / 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 / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / THIS DEPOSIT IS THE REFINEMENT OF THE PREVIOUSLY DETERMINED 1GC1 STRUCTURE / Resolution: 2.2 Å | |||||||||
Authors | Kwong, P.D. / Wyatt, R. / Majeed, S. / Robinson, J. / Sweet, R.W. / Sodroski, J. / Hendrickson, W.A. | |||||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. Authors: Kwong, P.D. / Wyatt, R. / Majeed, S. / Robinson, J. / Sweet, R.W. / Sodroski, J. / Hendrickson, W.A. #1: Journal: Nature / Year: 1998 Title: Structure of an HIV gp120 Envelope Glycoprotein in Complex with the CD4 Receptor and a Neutralizing Human Antibody Authors: Kwong, P.D. / Wyatt, R. / Robinson, J. / Sweet, R.W. / Sodroski, J. / Hendrickson, W.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g9m.cif.gz | 226.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g9m.ent.gz | 176.4 KB | Display | PDB format |
PDBx/mmJSON format | 1g9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/1g9m ftp://data.pdbj.org/pub/pdb/validation_reports/g9/1g9m | HTTPS FTP |
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-Related structure data
Related structure data | 1g9nC 1gc1S S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 2 types, 2 molecules GC
#1: Protein | Mass: 35429.094 Da / Num. of mol.: 1 / Fragment: CORE / Mutation: VARIABLE LOOPS SUBSTITUTED Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: CLADE B Description: SECRETED FROM DROSOPHILA SCHNEIDER 2 LINES UNDER CONTROL OF AN INDUCIBLE METALL OTHIONEIN PROMOTER Variant: LABORATORY-ADAPTED ISOLATE HXBC2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P04578 |
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#2: Protein | Mass: 20503.260 Da / Num. of mol.: 1 / Fragment: D1D2, N-TERMINAL TWO DOMAIN FRAGMENT / Mutation: S184N, I185T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): OVARY CELLS (CHO) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01730 |
-Antibody , 2 types, 2 molecules LH
#3: Antibody | Mass: 23439.961 Da / Num. of mol.: 1 / Fragment: ANTIGEN-BINDING FRAGMENT, FAB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: EPSTEIN-BARR VIRUS IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER Production host: Mus musculus (house mouse) |
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#4: Antibody | Mass: 24525.578 Da / Num. of mol.: 1 / Fragment: ANTIGEN-BINDING FRAGMENT, FAB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: EPSTEIN-BARR VIRUS IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER Production host: Mus musculus (house mouse) |
-Sugars , 2 types, 14 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 954 molecules
#7: Chemical | ChemComp-IPA / |
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#8: 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 Å3/Da / Density % sol: 59 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: VAPOUR DIFFUSION CRYSTALLIZATION: 0.5 UL OF PROTEIN (~10MG/ML IN 350 MM NACL, 5 MM TRISCL PH 7.0) + 0.4 UL OF 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, 0. ...Details: VAPOUR DIFFUSION CRYSTALLIZATION: 0.5 UL OF PROTEIN (~10MG/ML IN 350 MM NACL, 5 MM TRISCL PH 7.0) + 0.4 UL OF 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, 0.0075% SEAPREP AGAROSE, PH 6.4 OVER A RESERVOIR OF 0.35 M NACL, 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, PH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97953 Å |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: May 25, 1996 |
Radiation | Monochromator: silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97953 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 138810 / Num. obs: 56183 / % possible obs: 87.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -0.35 / Redundancy: 2.47 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.145 / Rsym value: 0.145 / Net I/σ(I): 5.33 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4207 / Rsym value: 0.382 / % possible all: 66.3 |
Reflection shell | *PLUS % possible obs: 66.3 % |
-Processing
Software |
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Refinement | Method to determine structure: THIS DEPOSIT IS THE REFINEMENT OF THE PREVIOUSLY DETERMINED 1GC1 STRUCTURE Starting model: pdb entry 1gc1 Resolution: 2.2→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: OVERALL ANISOTROPIC B VALUE CORRECTION APPLIED TO DATA DURING CNS REFINEMENT
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Solvent computation | Solvent model: flat model / Bsol: 52.7663 Å2 / ksol: 0.305424 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.21 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 50
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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