+Open data
-Basic information
Entry | Database: PDB / ID: 2gd5 | ||||||
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Title | Structural basis for budding by the ESCRTIII factor CHMP3 | ||||||
Components | Charged multivesicular body protein 3 | ||||||
Keywords | PROTEIN TRANSPORT / CHMP3 / ESCRT-III | ||||||
Function / homology | Function and homology information regulation of endosome size / 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 ...regulation of endosome size / 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 / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / multivesicular body sorting pathway / membrane fission / plasma membrane repair / phosphatidylcholine binding / multivesicular body membrane / late endosome to vacuole transport / 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 / regulation of early endosome to late endosome transport / mitotic metaphase chromosome alignment / Macroautophagy / molecular function inhibitor activity / ubiquitin-specific protease binding / nucleus organization / viral budding via host ESCRT complex / positive regulation of cytokinesis / autophagosome membrane / autophagosome maturation / viral release from host cell / protein polymerization / 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 / kinetochore / autophagy / late endosome / protein transport / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / cytoplasmic vesicle / early endosome / lysosomal membrane / apoptotic process / extracellular exosome / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Muziol, T.M. / Pineda-Molina, E. / Ravelli, R.B. / Zamborlini, A. / Usami, Y. / Gottlinger, H. / Weissenhorn, W. | ||||||
Citation | Journal: Dev.Cell / Year: 2006 Title: Structural Basis for Budding by the ESCRT-III Factor CHMP3. Authors: Pineda-Molina, E. / Ravelli, R.B. / Zamborlini, A. / Usami, Y. / Weissenhorn, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gd5.cif.gz | 125.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gd5.ent.gz | 107 KB | Display | PDB format |
PDBx/mmJSON format | 2gd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/2gd5 ftp://data.pdbj.org/pub/pdb/validation_reports/gd/2gd5 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 6
NCS ensembles :
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-Components
#1: Protein | Mass: 21001.621 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHMP3 / Plasmid: pProExHtb / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 codon + / References: UniProt: Q9Y3E7 |
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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: 2.35 Å3/Da / Density % sol: 47.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 8-12% PEG 3350, 200mM ammonium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97927 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jan 31, 2005 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97927 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→33 Å / Num. obs: 17853 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 63.075 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.33 |
Reflection shell | Resolution: 2.8→3 Å / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 4.98 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.907 / SU B: 42.655 / SU ML: 0.38 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.707 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.8→2.871 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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