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- PDB-3obu: Crystal structure of the Tsg101 UEV domain in complex with a HIV-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3obu | ||||||
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Title | Crystal structure of the Tsg101 UEV domain in complex with a HIV-1 PTAP peptide | ||||||
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![]() | PROTEIN TRANSPORT / Protein tranport / ubiquitin / HIV-1 Gag | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Im, Y.J. / Hurley, J.H. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.3 KB | Display | ![]() |
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PDB format | ![]() | 31.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.9 KB | Display | ![]() |
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Full document | ![]() | 434 KB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3obqC ![]() 3obsC ![]() 3obxC ![]() 2f0rS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 965.997 Da / Num. of mol.: 1 / Fragment: HIV-1 Gag PTAP motif (5-13) / Source method: obtained synthetically Details: This sequence occurs naturally in human immunodeficiency virus type 1. References: UniProt: Q72497 |
#3: Water | ChemComp-HOH / |
Sequence details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.45 % |
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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: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2010 / 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: 18250 / Num. obs: 17689 / % possible obs: 98.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.6 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 4.1 / Num. unique all: 799 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2F0R Resolution: 1.6→42.72 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 874513.6 / 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: 39.613 Å2 / ksol: 0.358431 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→42.72 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: 0.024 / Total num. of bins used: 6
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Xplor file |
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