+Open data
-Basic information
Entry | Database: PDB / ID: 4u7y | ||||||
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Title | Structure of the complex of VPS4B MIT and IST1 MIM | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / complex / MIM1 | ||||||
Function / homology | Function and homology information protein depolymerization / positive regulation of centriole elongation / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / negative regulation of exosomal secretion / viral capsid secondary envelopment / MIT domain binding / late endosome to lysosome transport via multivesicular body sorting pathway / abscission / ESCRT III complex disassembly / late endosomal microautophagy ...protein depolymerization / positive regulation of centriole elongation / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / negative regulation of exosomal secretion / viral capsid secondary envelopment / MIT domain binding / late endosome to lysosome transport via multivesicular body sorting pathway / abscission / ESCRT III complex disassembly / late endosomal microautophagy / cytoskeleton-dependent cytokinesis / collateral sprouting / regulation of centrosome duplication / Sealing of the nuclear envelope (NE) by ESCRT-III / nuclear membrane reassembly / positive regulation of collateral sprouting / midbody abscission / establishment of blood-brain barrier / vacuole organization / multivesicular body sorting pathway / membrane fission / plasma membrane repair / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / cholesterol transport / endosome to lysosome transport via multivesicular body sorting pathway / multivesicular body assembly / regulation of mitotic spindle assembly / vesicle-fusing ATPase / Flemming body / nucleus organization / endosomal transport / mitotic metaphase chromosome alignment / ATPase complex / response to lipid / viral budding via host ESCRT complex / autophagosome maturation / positive regulation of proteolysis / viral release from host cell / endoplasmic reticulum-Golgi intermediate compartment / canonical Wnt signaling pathway / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / positive regulation of G2/M transition of mitotic cell cycle / viral budding from plasma membrane / macroautophagy / establishment of protein localization / Budding and maturation of HIV virion / protein localization / potassium ion transport / autophagy / spindle pole / azurophil granule lumen / protein transport / nuclear envelope / late endosome membrane / midbody / angiogenesis / endosome membrane / endosome / cadherin binding / cell division / protein domain specific binding / intracellular membrane-bounded organelle / centrosome / chromatin / Neutrophil degranulation / protein-containing complex binding / ATP hydrolysis activity / protein homodimerization activity / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å | ||||||
Authors | Guo, E.Z. / Xu, Z. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Distinct Mechanisms of Recognizing Endosomal Sorting Complex Required for Transport III (ESCRT-III) Protein IST1 by Different Microtubule Interacting and Trafficking (MIT) Domains. Authors: Guo, E.Z. / Xu, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u7y.cif.gz | 32.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u7y.ent.gz | 19.6 KB | Display | PDB format |
PDBx/mmJSON format | 4u7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/4u7y ftp://data.pdbj.org/pub/pdb/validation_reports/u7/4u7y | HTTPS FTP |
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-Related structure data
Related structure data | 4u7eC 4u7iC 1wr0S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10310.705 Da / Num. of mol.: 1 / Fragment: MIT domain (UNP residues 1-89) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VPS4B, SKD1, VPS42, MIG1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: O75351, vesicle-fusing ATPase |
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#2: Protein/peptide | Mass: 3009.262 Da / Num. of mol.: 1 / Fragment: UNP residues 341-364 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IST1, KIAA0174 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P53990 |
#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: 2.25 Å3/Da / Density % sol: 45.4 % |
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Crystal grow | Temperature: 299 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 2.58 M Na-malonate / PH range: 5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 19, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→33.82 Å / Num. obs: 4455 / % possible obs: 96.9 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 21.1 |
Reflection shell | Redundancy: 12.7 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 6.4 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WR0 Resolution: 2.502→33.82 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 28.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.502→33.82 Å
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Refine LS restraints |
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LS refinement shell |
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