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Yorodumi- PDB-2pjw: The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pjw | ||||||
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Title | The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting | ||||||
Components |
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Keywords | ENDOCYTOSIS/EXOCYTOSIS / GAT domain / Core complex / Doamin Swap / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | Function and homology information microlipophagy / positive regulation of protein maturation / ESCRT-0 complex / microautophagy / protein retention in Golgi apparatus / ATP export / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to vacuole / multivesicular body sorting pathway / late endosome to vacuole transport ...microlipophagy / positive regulation of protein maturation / ESCRT-0 complex / microautophagy / protein retention in Golgi apparatus / ATP export / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to vacuole / multivesicular body sorting pathway / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding / cellular response to nitrogen starvation / vacuolar membrane / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / protein secretion / ubiquitin binding / endosome / endosome membrane / protein domain specific binding / protein heterodimerization activity / protein-containing complex / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / TWO WAVELENGTH MAD / Resolution: 3.01 Å | ||||||
Authors | Prag, G. / Hurley, J.H. | ||||||
Citation | Journal: Dev.Cell / Year: 2007 Title: The Vps27/Hse1 Complex Is a GAT Domain-Based Scaffold for Ubiquitin-Dependent Sorting. Authors: Prag, G. / Watson, H. / Kim, Y.C. / Beach, B.M. / Ghirlando, R. / Hummer, G. / Bonifacino, J.S. / Hurley, J.H. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Structural mechanism for ubiquitinated-cargo recognition by the Golgi-localized, {gamma}-ear-containing, ADP-ribosylation-factor-binding proteins Authors: Prag, G. / Lee, S. / Mattera, R. / Arighi, C.N. / Beach, B.M. / Bonifacino, J.S. / Hurley, J.H. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pjw.cif.gz | 45.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pjw.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 2pjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pjw_validation.pdf.gz | 433.5 KB | Display | wwPDB validaton report |
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Full document | 2pjw_full_validation.pdf.gz | 443.1 KB | Display | |
Data in XML | 2pjw_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 2pjw_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/2pjw ftp://data.pdbj.org/pub/pdb/validation_reports/pj/2pjw | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar 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
#1: Protein | Mass: 10049.697 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: hse1 / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P38753 |
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#2: Protein | Mass: 10770.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: VPS27, GRD11 / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P40343 |
#3: 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: 2.32 Å3/Da / Density % sol: 46.91 % Description: The structure factor file contains Friedel pairs. |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 8.85 Details: 1.1-1.4 M ammonium sulfate, 0.1 M Tris-HCl. Then micro-seeding into 1.25 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.85, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 95 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979493, 0.972425 | |||||||||
Detector | Detector: CCD / Date: Jul 12, 2006 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 3.01→46.92 Å / Num. obs: 7506 / Redundancy: 4.1 % / Rsym value: 0.052 / Net I/σ(I): 18.1 | |||||||||
Reflection shell | Resolution: 3.01→3.14 Å |
-Processing
Software |
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Refinement | Method to determine structure: TWO WAVELENGTH MAD / Resolution: 3.01→46.92 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 276902.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: BULK SOLVENT MODEL USED. The Friedel pairs were used for phasing.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 69.289 Å2 / ksol: 0.370494 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.01→46.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.062 / Total num. of bins used: 6
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