[English] 日本語
Yorodumi- PDB-4txr: Crystal structure of LIP5 N-terminal domain complexed with CHMP1B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4txr | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM and CHMP5 MIM | |||||||||
Components |
| |||||||||
Keywords | PROTEIN TRANSPORT / MIT domain / MIM / ESCRT | |||||||||
Function / homology | Function and homology information MIT domain binding / amphisome membrane / multivesicular body-lysosome fusion / viral budding / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway ...MIT domain binding / amphisome membrane / multivesicular body-lysosome fusion / viral budding / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / regulation of centrosome duplication / cellular response to muramyl dipeptide / nuclear membrane reassembly / midbody abscission / multivesicular body sorting pathway / vesicle budding from membrane / membrane fission / plasma membrane repair / membrane coat / 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 / mitotic metaphase chromosome alignment / nucleus organization / viral budding via host ESCRT complex / autophagosome membrane / autophagosome maturation / regulation of receptor recycling / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / erythrocyte differentiation / viral budding from plasma membrane / macroautophagy / establishment of protein localization / Budding and maturation of HIV virion / kinetochore / autophagy / protein transport / midbody / cellular response to lipopolysaccharide / endosome membrane / cadherin binding / lysosomal membrane / protein domain specific binding / cell division / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | |||||||||
Authors | Vild, C.J. / Xu, Z. | |||||||||
Funding support | United States, 1items
| |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: A Novel Mechanism of Regulating the ATPase VPS4 by Its Cofactor LIP5 and the Endosomal Sorting Complex Required for Transport (ESCRT)-III Protein CHMP5. Authors: Vild, C.J. / Li, Y. / Guo, E.Z. / Liu, Y. / Xu, Z. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4txr.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4txr.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 4txr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/4txr ftp://data.pdbj.org/pub/pdb/validation_reports/tx/4txr | HTTPS FTP |
---|
-Related structure data
Related structure data | 4txpC 4txqSC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Charged multivesicular body protein ... , 2 types, 2 molecules BC
#1: Protein/peptide | Mass: 2718.953 Da / Num. of mol.: 1 / Fragment: UNP residues 176-199 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHMP1B, C18orf2 / Plasmid: pSMT3 Details (production host): modified pET28B; his6-SUMO tag; kanR Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q7LBR1 |
---|---|
#3: Protein | Mass: 6188.371 Da / Num. of mol.: 1 / Fragment: UNP residues 139-195 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: CHMP5, C9orf83, SNF7DC2, CGI-34, HSPC177, PNAS-114, PNAS-2 Plasmid: pSMT3 Details (production host): modified pET28B; his6-SUMO tag; kanR Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9NZZ3 |
-Protein , 1 types, 1 molecules A
#2: Protein | Mass: 18792.727 Da / Num. of mol.: 1 / Fragment: UNP residues 1-162 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VTA1, C6orf55, HSPC228, My012 / Plasmid: pSMT3 Details (production host): modified pET28B; his6-SUMO tag; kanR Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9NP79 |
---|
-Non-polymers , 3 types, 289 molecules
#4: Chemical | ChemComp-ACT / | ||
---|---|---|---|
#5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.42 % Description: approximately 150 nanometer large diamond shaped crystal |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 19% PEG 4000, 0.025 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 193.15 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.99983 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2013 |
Radiation | Monochromator: diamond laue monochromators with beryllium lenses Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99983 Å / Relative weight: 1 |
Reflection | Resolution: 1→28.68 Å / Num. obs: 99846 / % possible obs: 87.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 50.6 |
Reflection shell | Resolution: 1→1.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.5 / % possible all: 46.1 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: dev_1593) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TXQ Resolution: 1→28.668 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.57 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→28.668 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|