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- PDB-2j9u: 2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus ... -
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Open data
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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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![]() | PROTEIN TRANSPORT / ZINC-FINGER / METAL-BINDING | ||||||
Function / homology | ![]() ESCRT II complex / carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / ESCRT I complex / ATP export / 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 / protein targeting to vacuole / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ...ESCRT II complex / carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / ESCRT I complex / ATP export / 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 / protein targeting to vacuole / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding / protein targeting to membrane / localization / ubiquitin binding / macroautophagy / late endosome membrane / endosome / protein-containing complex binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gill, D.J. / Teo, H.L. / Sun, J. / Perisic, O. / Veprintsev, D.B. / Emr, S.D. / Williams, R.L. | ||||||
![]() | ![]() Title: 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.9 KB | Display | ![]() |
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PDB format | ![]() | 57.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.6 KB | Display | ![]() |
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Full document | ![]() | 467.6 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | 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: ![]() |
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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: ![]() ![]() ![]() |
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: ![]() Starting 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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