+Open data
-Basic information
Entry | Database: PDB / ID: 2xze | ||||||
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Title | Structural basis for AMSH-ESCRT-III CHMP3 interaction | ||||||
Components |
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Keywords | HYDROLASE/PROTEIN TRANSPORT / HYDROLASE-PROTEIN TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information regulation of endosome size / negative regulation of hippocampal neuron apoptotic process / hippocampal neuron apoptotic process / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / suppression of viral release by host / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule ...regulation of endosome size / negative regulation of hippocampal neuron apoptotic process / hippocampal neuron apoptotic process / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / suppression of viral release by host / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / regulation of centrosome duplication / nuclear membrane reassembly / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / Sealing of the nuclear envelope (NE) by ESCRT-III / deubiquitinase activity / midbody abscission / multivesicular body sorting pathway / membrane fission / plasma membrane repair / late endosome to vacuole transport / phosphatidylcholine binding / multivesicular body membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / regulation of mitotic spindle assembly / negative regulation of Ras protein signal transduction / metal-dependent deubiquitinase activity / Translation of Replicase and Assembly of the Replication Transcription Complex / K63-linked deubiquitinase activity / regulation of early endosome to late endosome transport / mitotic metaphase chromosome alignment / Macroautophagy / molecular function inhibitor activity / nucleus organization / ubiquitin-specific protease binding / protein deubiquitination / viral budding via host ESCRT complex / positive regulation of cytokinesis / cell surface receptor signaling pathway via JAK-STAT / autophagosome membrane / cleavage furrow / autophagosome maturation / viral release from host cell / mitotic cytokinesis / protein polymerization / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Pyroptosis / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / phosphatidylinositol-4,5-bisphosphate binding / multivesicular body / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / Metalloprotease DUBs / kinetochore / autophagy / protein transport / late endosome / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / cytoplasmic vesicle / early endosome / endosome / protein domain specific binding / lysosomal membrane / apoptotic process / positive regulation of cell population proliferation / proteolysis / extracellular exosome / nucleoplasm / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å | ||||||
Authors | Solomons, J. / Sabin, C. / Weissenhorn, W. | ||||||
Citation | Journal: Structure / Year: 2011 Title: Structural Basis for Escrt-III Chmp3 Recruitment of Amsh. Authors: Solomons, J. / Sabin, C. / Poudevigne, E. / Usami, Y. / Hulsik, D.L. / Macheboeuf, P. / Hartlieb, B. / Gottlinger, H. / Weissenhorn, W. #1: Journal: J.Mol.Biol. / Year: 2008 Title: Structural Basis for Autoinhibition of Escrt-III Chmp3. Authors: Lata, S. / Roessle, M. / Solomons, J. / Jamin, M. / Gottlinger, H.G. / Svergun, D.I. / Weissenhorn, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xze.cif.gz | 85.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xze.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xze_validation.pdf.gz | 450.3 KB | Display | wwPDB validaton report |
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Full document | 2xze_full_validation.pdf.gz | 453.3 KB | Display | |
Data in XML | 2xze_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 2xze_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/2xze ftp://data.pdbj.org/pub/pdb/validation_reports/xz/2xze | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 17162.611 Da / Num. of mol.: 2 / Fragment: MIT DOMAIN, RESIDUES 1-146 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: O95630, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases #2: Protein/peptide | Mass: 4331.674 Da / Num. of mol.: 2 / Fragment: C-TERM FRAGMENT, RESIDUES 183-222 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9Y3E7 #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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 6 Details: 3.3 MG/ML OF AMSH PROTEIN IN 10 MM HEPES PH 8.0, 100 MM NACL WAS MIXED WITH AN EQUAL VOLUME WELL CONDITION: 2.2 M SODIUM MALONATE,WITH 30 % GLYCEROL AS CRYO-PROTECTANT |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9760, 0.9795 | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2009 / Details: TORODIAL FOCUSING MIRROR | |||||||||
Radiation | Monochromator: U35 UNDULATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→44.85 Å / Num. obs: 141404 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.1 | |||||||||
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.2 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.75→51.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.52 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.111 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.212 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→51.71 Å
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