+Open data
-Basic information
Entry | Database: PDB / ID: 3frt | ||||||
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Title | The structure of human CHMP3 (residues 8 - 222). | ||||||
Components | Charged multivesicular body protein 3 | ||||||
Keywords | PROTEIN TRANSPORT / ESCRT / ESCRT-111 / CHMP / Ist1 / Coiled coil / Cytoplasm / Lipoprotein / Membrane / Myristate / Phosphoprotein / Transport | ||||||
Function / homology | Function and homology information regulation of endosome size / amphisome membrane / multivesicular body-lysosome fusion / suppression of viral release by host / vesicle fusion with vacuole / 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 / suppression of viral release by host / vesicle fusion with vacuole / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / regulation of centrosome duplication / Sealing of the nuclear envelope (NE) by ESCRT-III / nuclear membrane reassembly / midbody abscission / multivesicular body sorting pathway / membrane fission / plasma membrane repair / phosphatidylcholine binding / late endosome to vacuole transport / 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 / nucleus organization / regulation of early endosome to late endosome transport / Macroautophagy / mitotic metaphase chromosome alignment / molecular function inhibitor activity / ubiquitin-specific protease binding / viral budding via host ESCRT complex / positive regulation of cytokinesis / autophagosome maturation / autophagosome membrane / protein polymerization / viral release from host cell / 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 / protein transport / late endosome / 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 / MOLECULAR REPLACEMENT / Resolution: 4 Å | ||||||
Authors | Schubert, H.L. / McCullough, J. / Hill, C.P. / Sundquist, W.I. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 Title: Structural basis for ESCRT-III protein autoinhibition. Authors: Bajorek, M. / Schubert, H.L. / McCullough, J. / Langelier, C. / Eckert, D.M. / Stubblefield, W.M. / Uter, N.T. / Myszka, D.G. / Hill, C.P. / Sundquist, W.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3frt.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3frt.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 3frt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/3frt ftp://data.pdbj.org/pub/pdb/validation_reports/fr/3frt | HTTPS FTP |
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-Related structure data
Related structure data | 3frrC 3frsC 3frvC 2gd5S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24700.600 Da / Num. of mol.: 2 / Fragment: UNP residues 8-222 Source method: isolated from a genetically manipulated source Details: N-term GST / Source: (gene. exp.) Homo sapiens (human) / Gene: CGI-149, CHMP3, NEDF, VPS24 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+RIL / 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: 2.24 Å3/Da / Density % sol: 45.06 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10-22% PEG 6000 0.1 M Hepes, pH 7.0-8.0, VAPOR DIFFUSION, SITTING DROP, temperature 286K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97607 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 27, 2008 Details: flat mirror (vertical), single crystal Si(iii) bent (horizonatal) |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97607 Å / Relative weight: 1 |
Reflection | Resolution: 4→30 Å / Num. obs: 2950 / % possible obs: 78.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 111 Å2 / Rmerge(I) obs: 0.16 / Rsym value: 0.185 / Net I/σ(I): 9.33 |
Reflection shell | Resolution: 4→4.14 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.92 / Num. unique all: 164 / Rsym value: 0.259 / % possible all: 78.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GD5 Resolution: 4→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: rigid body only - against anisotropically adjusted Fs by PHASER.
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Refinement step | Cycle: LAST / Resolution: 4→30 Å
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