+Open data
-Basic information
Entry | Database: PDB / ID: 3htu | ||||||
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Title | Crystal structure of the human VPS25-VPS20 subcomplex | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / ESCRT-II / ESCRT-III / VPS20 / VPS25 / MVB / Cytoplasm / Nucleus / Polymorphism / Transcription / Transcription regulation / Transport / Coiled coil / Endosome / Lipoprotein / Membrane / Myristate | ||||||
Function / homology | Function and homology information ESCRT III complex assembly / ESCRT II complex / negative regulation of epidermal growth factor-activated receptor activity / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ...ESCRT III complex assembly / ESCRT II complex / negative regulation of epidermal growth factor-activated receptor activity / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / multivesicular body sorting pathway / vesicle budding from membrane / membrane fission / plasma membrane repair / multivesicular body membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / regulation of mitotic spindle assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / mitotic metaphase chromosome alignment / Macroautophagy / nucleus organization / regulation of protein catabolic process / viral budding via host ESCRT complex / autophagosome membrane / autophagosome maturation / Pyroptosis / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / kinetochore / autophagy / protein transport / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / endosome membrane / lysosomal membrane / intracellular membrane-bounded organelle / protein-containing complex binding / structural molecule activity / protein homodimerization activity / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Im, Y.J. / Hurley, J.H. | ||||||
Citation | Journal: Dev.Cell / Year: 2009 Title: Structure and function of the ESCRT-II-III interface in multivesicular body biogenesis. Authors: Im, Y.J. / Wollert, T. / Boura, E. / 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 | 3htu.cif.gz | 194.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3htu.ent.gz | 157.1 KB | Display | PDB format |
PDBx/mmJSON format | 3htu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/3htu ftp://data.pdbj.org/pub/pdb/validation_reports/ht/3htu | HTTPS FTP |
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-Related structure data
Related structure data | 3cuoS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 9024.925 Da / Num. of mol.: 4 Fragment: The C-terminal WH2 domain of VPS25: UNP residues 102-176 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DERP9, EAP20, VPS25 / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q9BRG1 #2: Protein/peptide | Mass: 4704.398 Da / Num. of mol.: 4 / Fragment: The first helix of VPS20: UNP residues 11-48 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHMP6, VPS20 / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q96FZ7 #3: Water | ChemComp-HOH / | |
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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: 2.1 Å3/Da / Density % sol: 41.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris-HCl pH 8.0, 35% PEG 4000, 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: MAR CCD 165 mm / Detector: CCD / Date: Nov 6, 2008 / 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: 2→50 Å / Num. all: 31046 / Num. obs: 30553 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rsym value: 0.059 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.03 / Num. unique all: 2678 / Rsym value: 0.281 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3CUO Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.91 / SU B: 10.97 / SU ML: 0.142 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.204 / 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: 32.521 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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