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Yorodumi- PDB-1rzk: HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDU... -
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-Basic information
Entry | Database: PDB / ID: 1rzk | |||||||||
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Title | HIV-1 YU2 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 / 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 ...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 / extracellular matrix structural constituent / T cell receptor complex / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Dectin-2 family / 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 / positive regulation of establishment of T cell polarity / T cell activation / positive regulation of interleukin-2 production / protein tyrosine kinase binding / host cell endosome membrane / Vpu mediated degradation of CD4 / calcium-mediated signaling / cell surface receptor protein tyrosine kinase signaling pathway / clathrin-coated endocytic vesicle membrane / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of T cell activation / Cargo recognition for clathrin-mediated endocytosis / Downstream TCR signaling / virus receptor activity / MHC class II protein complex binding / Clathrin-mediated endocytosis / signaling receptor activity / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / defense response to Gram-negative bacterium / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / early endosome / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / viral protein processing / cell adhesion / immune response / membrane raft / positive regulation of protein phosphorylation / fusion of virus membrane with host plasma membrane / external side of plasma membrane / virus-mediated perturbation of host defense response / endoplasmic reticulum lumen / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / endoplasmic reticulum membrane / virion attachment to host cell / protein kinase binding / host cell plasma membrane / virion membrane / structural molecule activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Huang, C.C. / Venturi, M. / Majeed, S. / Moore, M.J. / Phogat, S. / Zhang, M.-Y. / Dimitrov, D.S. / Hendrickson, W.A. / Robinson, J. / Sodroski, J. ...Huang, C.C. / Venturi, M. / Majeed, S. / Moore, M.J. / Phogat, S. / Zhang, M.-Y. / Dimitrov, D.S. / Hendrickson, W.A. / Robinson, J. / Sodroski, J. / Wyatt, R. / Choe, H. / Farzan, M. / Kwong, P.D. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120 Authors: Huang, C.C. / Venturi, M. / Majeed, S. / Moore, M.J. / Phogat, S. / Zhang, M.-Y. / Dimitrov, D.S. / Hendrickson, W.A. / Robinson, J. / Sodroski, J. / Wyatt, R. / Choe, H. / Farzan, M. / Kwong, P.D. #1: Journal: Structure / 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rzk.cif.gz | 208.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rzk.ent.gz | 163.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/1rzk ftp://data.pdbj.org/pub/pdb/validation_reports/rz/1rzk | HTTPS FTP |
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-Related structure data
Related structure data | 1rz7C 1rz8C 1rzfC 1rzgC 1rziC 1rzjC 1g9mS C: citing same article (ref.) 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
-Protein , 2 types, 2 molecules GC
#1: Protein | Mass: 34838.691 Da / Num. of mol.: 1 / Fragment: CORE / Mutation: VARIABLE LOOPS SUBSTITUTED Source method: isolated from a genetically manipulated source Details: part of Envelope polyprotein GP160 / Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: CLADE B Description: SECRETED FROM DROSOPHILA SCHNEIDER 2 LINES UNDER CONTROL OF AN INDUCIBLE METALLOTHIONEIN PROMOTER; Variant: LABORATORY-ADAPTED ISOLATE HXBC2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P35961*PLUS |
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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: 23399.898 Da / Num. of mol.: 1 / Fragment: FAB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Genus (production host): Lymphocryptovirus Cell (production host): IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER Production host: Human herpesvirus 4 (Epstein-Barr virus) |
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#4: Antibody | Mass: 24457.387 Da / Num. of mol.: 1 / Fragment: FAB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Genus (production host): Lymphocryptovirus Cell (production host): IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER Production host: Human herpesvirus 4 (Epstein-Barr virus) |
-Sugars / Non-polymers , 2 types, 358 molecules
#5: Sugar | ChemComp-NAG / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 49.8 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 0.5 UL OF PROTEIN (5 MG/ML IN 0.35 M NACL, 0.005 M TRIS CL PH 7.0) + 0.35 UL OF RESERVOIR (50 UL OF NA ACETATE PH 4.5 + 250 UL OF HAMPTON CRYSTAL SCREEN REAGENT 18 + 126 UL OF ETHANOL + 292 ...Details: 0.5 UL OF PROTEIN (5 MG/ML IN 0.35 M NACL, 0.005 M TRIS CL PH 7.0) + 0.35 UL OF RESERVOIR (50 UL OF NA ACETATE PH 4.5 + 250 UL OF HAMPTON CRYSTAL SCREEN REAGENT 18 + 126 UL OF ETHANOL + 292 UL OF WATER), pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
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: 0.9721 / Wavelength: 0.9721 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 26, 2000 |
Radiation | Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9721 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. obs: 23464 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.37 % / Biso Wilson estimate: 86 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 10.38 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.33 / Rsym value: 0.439 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G9M Resolution: 2.9→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 273749.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 15.6679 Å2 / ksol: 0.219388 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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