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Yorodumi- PDB-3obx: Crystal structure of the Tsg101 UEV domain in complex with a HIV-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3obx | ||||||
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Title | Crystal structure of the Tsg101 UEV domain in complex with a HIV-1 Gag P7A mutant peptide | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / Protein tranport / ubiquitin / HIV-1 Gag | ||||||
Function / homology | Function and homology information positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / viral budding / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ...positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / viral budding / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / membrane fission / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / Flemming body / virion binding / endosome to lysosome transport / negative regulation of epidermal growth factor receptor signaling pathway / viral budding via host ESCRT complex / autophagosome maturation / viral release from host cell / keratinocyte differentiation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / HCMV Late Events / ubiquitin binding / regulation of cell growth / macroautophagy / Late endosomal microautophagy / protein modification process / Budding and maturation of HIV virion / transcription corepressor activity / calcium-dependent protein binding / late endosome / late endosome membrane / early endosome membrane / viral nucleocapsid / host cell cytoplasm / early endosome / endosome membrane / regulation of cell cycle / endosome / cell cycle / negative regulation of cell population proliferation / cell division / centrosome / ubiquitin protein ligase binding / host cell nucleus / protein-containing complex binding / nucleolus / structural molecule activity / virion membrane / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / RNA binding / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Im, Y.J. / Hurley, J.H. | ||||||
Citation | Journal: Structure / Year: 2010 Title: Crystallographic and Functional Analysis of the ESCRT-I /HIV-1 Gag PTAP Interaction. Authors: Im, Y.J. / Kuo, L. / Ren, X. / Burgos, P.V. / Zhao, X.Z. / Liu, F. / Burke, T.R. / Bonifacino, J.S. / Freed, E.O. / Hurley, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3obx.cif.gz | 46.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3obx.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 3obx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3obx_validation.pdf.gz | 429.5 KB | Display | wwPDB validaton report |
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Full document | 3obx_full_validation.pdf.gz | 430.8 KB | Display | |
Data in XML | 3obx_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 3obx_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/3obx ftp://data.pdbj.org/pub/pdb/validation_reports/ob/3obx | HTTPS FTP |
-Related structure data
Related structure data | 3obqC 3obsC 3obuSC 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
#1: Protein | Mass: 16501.195 Da / Num. of mol.: 1 / Fragment: N-terminal UEV domain (UNP residues 2 to 145) / Mutation: 43VFNDGS48 -> GTG Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TSG101 / Plasmid: pGST2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) star / References: UniProt: Q99816 |
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#2: Protein/peptide | Mass: 939.960 Da / Num. of mol.: 1 / Fragment: HIV-1 Gag PTAP motif (5-13) / Mutation: P7A mutant / Source method: obtained synthetically / Details: P7A mutation of HIV-1 Gag p6 peptide / References: UniProt: Q72497 |
#3: Water | ChemComp-HOH / |
Sequence details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES-NaOH (pH7.5), 25% PEG 3350, 0.2M Sodium Nitrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 9, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 18620 / Num. obs: 18234 / % possible obs: 97.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.4 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 6.6 / Num. unique all: 826 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3OBU Resolution: 1.6→31.9 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 874549.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.3207 Å2 / ksol: 0.342914 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→31.9 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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