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Yorodumi- PDB-2b4c: Crystal structure of HIV-1 JR-FL gp120 core protein containing th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b4c | |||||||||
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Title | Crystal structure of HIV-1 JR-FL gp120 core protein containing the third variable region (V3) complexed with CD4 and the X5 antibody | |||||||||
Components |
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Keywords | Viral protein/Immune system / HIV-1 / gp120 / JRFL / V3 / X5 / CD4 induced antibody / 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 / 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 plasma membrane raft polarization / positive regulation of receptor clustering / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of establishment of T cell polarity / T cell activation / positive regulation of calcium-mediated signaling / positive regulation of interleukin-2 production / protein tyrosine kinase binding / host cell endosome membrane / clathrin-coated endocytic vesicle membrane / Vpu mediated degradation of CD4 / calcium-mediated signaling / transmembrane signaling receptor activity / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of T cell activation / Clathrin-mediated endocytosis / virus receptor activity / Downstream TCR signaling / MHC class II protein complex binding / signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / clathrin-dependent endocytosis of virus by host cell / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / cell surface receptor signaling pathway / positive regulation of viral entry into host cell / early endosome / viral protein processing / cell adhesion / positive regulation of protein phosphorylation / membrane raft / immune response / endoplasmic reticulum lumen / external side of plasma membrane / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / virion attachment to host cell / protein kinase binding / apoptotic process / enzyme binding / structural molecule activity / host cell plasma membrane / virion membrane / signal transduction / protein homodimerization activity / zinc ion binding / 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: 3.3 Å | |||||||||
Authors | Huang, C. / Tang, M. / Zhang, M.Y. / Majeed, S. / Montabana, E. / Stanfield, R.L. / Dimitrov, D.S. / Korber, B. / Sodroski, J. / Wilson, I.A. ...Huang, C. / Tang, M. / Zhang, M.Y. / Majeed, S. / Montabana, E. / Stanfield, R.L. / Dimitrov, D.S. / Korber, B. / Sodroski, J. / Wilson, I.A. / Wyatt, R. / Kwong, P.D. | |||||||||
Citation | Journal: Science / Year: 2005 Title: Structure of a V3-containing HIV-1 gp120 core. Authors: Huang, C.C. / Tang, M. / Zhang, M.Y. / Majeed, S. / Montabana, E. / Stanfield, R.L. / Dimitrov, D.S. / Korber, B. / Sodroski, J. / Wilson, I.A. / Wyatt, R. / Kwong, P.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b4c.cif.gz | 205.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b4c.ent.gz | 160.1 KB | Display | PDB format |
PDBx/mmJSON format | 2b4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/2b4c ftp://data.pdbj.org/pub/pdb/validation_reports/b4/2b4c | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules GC
#1: Protein | Mass: 38452.652 Da / Num. of mol.: 1 / Fragment: CORE with V3 / Mutation: N301Q, T389A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Drosophila melanogaster (fruit fly) / References: GenBank: 1465781, UniProt: Q75760*PLUS |
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#2: Protein | Mass: 20129.896 Da / Num. of mol.: 1 / Fragment: D1D2, N-TERMINAL TWO DOMAIN FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD4 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01730 |
-Antibody , 2 types, 2 molecules LH
#3: Antibody | Mass: 23267.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#4: Antibody | Mass: 24990.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-Sugars , 3 types, 7 molecules
#5: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#6: Sugar | #8: Sugar | |
-Non-polymers , 1 types, 5 molecules
#7: Chemical | ChemComp-SO4 / |
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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: 3.28 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 293 K / pH: 5.5 Details: ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 12, 2004 |
Radiation | Monochromator: SI (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→20 Å / Num. obs: 19372 / % possible obs: 86.6 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.505 / % possible all: 20.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RHH AND 1RZK Resolution: 3.3→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 8776198.43 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 126.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.51 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
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