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Yorodumi- PDB-2j9u: 2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus ... -
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Basic information
| Entry | Database: PDB / ID: 2j9u | ||||||
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| Title | 2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus in complex with the NZF-N domain from ESCRT-II | ||||||
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Keywords | PROTEIN TRANSPORT / ZINC-FINGER / METAL-BINDING | ||||||
| Function / homology | Function and homology informationESCRT II complex / ESCRT I complex / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / cytoplasm to vacuole targeting by the Cvt pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ATP export / protein targeting to vacuole / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding ...ESCRT II complex / ESCRT I complex / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / cytoplasm to vacuole targeting by the Cvt pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ATP export / protein targeting to vacuole / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding / protein targeting to membrane / ubiquitin binding / macroautophagy / late endosome membrane / endosome / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / cytosol Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Gill, D.J. / Teo, H.L. / Sun, J. / Perisic, O. / Veprintsev, D.B. / Emr, S.D. / Williams, R.L. | ||||||
Citation | Journal: Embo J. / Year: 2007Title: Structural Insight Into the Escrt-I/-II Link and its Role in Mvb Trafficking. Authors: Gill, D.J. / Teo, H.L. / Sun, J. / Perisic, O. / Veprintsev, D.B. / Emr, S.D. / Williams, R.L. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2j9u.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2j9u.ent.gz | 57.3 KB | Display | PDB format |
| PDBx/mmJSON format | 2j9u.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 2j9u_validation.pdf.gz | 460.6 KB | Display | wwPDB validaton report |
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| Full document | 2j9u_full_validation.pdf.gz | 467.6 KB | Display | |
| Data in XML | 2j9u_validation.xml.gz | 13.3 KB | Display | |
| Data in CIF | 2j9u_validation.cif.gz | 17.5 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/2j9u ftp://data.pdbj.org/pub/pdb/validation_reports/j9/2j9u | HTTPS FTP |
-Related structure data
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Links
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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| 2 | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
NCS ensembles :
NCS oper:
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Components
| #1: Protein | Mass: 11151.820 Da / Num. of mol.: 2 / Fragment: RESIDUES 148-242 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: POPC / Production host: ![]() #2: Protein | Mass: 8315.310 Da / Num. of mol.: 2 / Fragment: RESIDUES 110-176 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: POPC / Production host: ![]() #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | INITIAL METHIONINE NOT NATIVE TO VPS28 SEQUENCE MAH6 AFFINITY TAG AND VPS36 RESIDUES 162-176 WERE ...INITIAL METHIONINE | |
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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: 2.16 Å3/Da / Density % sol: 49.7 % |
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| Crystal grow | pH: 7.4 / Details: 20% ETHANOL, 0.1M KCL, pH 7.40 |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.873 |
| Detector | Type: MARRESEARCH / Detector: CCD / Date: May 14, 2006 / Details: BENT MIRRORS |
| Radiation | Monochromator: SI3 MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
| Reflection | Resolution: 2→55.47 Å / Num. obs: 32191 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.02 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.2 |
| Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6.17 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.4 / % possible all: 99.9 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: ZN PEAK DATASET FROM NATIVE CRYSTAL Resolution: 2→32.03 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.892 / SU B: 7.221 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 23.39 Å2
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| Refinement step | Cycle: LAST / Resolution: 2→32.03 Å
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| Refine LS restraints |
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