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- PDB-2zme: Integrated structural and functional model of the human ESCRT-II ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zme | ||||||
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Title | Integrated structural and functional model of the human ESCRT-II complex | ||||||
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![]() | PROTEIN TRANSPORT / ESCRT / Sorting / MBV / vps / Nucleus / Transcription / Transcription regulation / Transport / Endosome / Lipid-binding | ||||||
Function / homology | ![]() ESCRT II complex / negative regulation of epidermal growth factor-activated receptor activity / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / regulation of protein complex stability / multivesicular body sorting pathway / membrane fission / early endosome to late endosome transport / positive regulation of exosomal secretion / multivesicular body assembly / channel regulator activity ...ESCRT II complex / negative regulation of epidermal growth factor-activated receptor activity / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / regulation of protein complex stability / multivesicular body sorting pathway / membrane fission / early endosome to late endosome transport / positive regulation of exosomal secretion / multivesicular body assembly / channel regulator activity / phosphatidylinositol-3-phosphate binding / endocytic recycling / regulation of protein catabolic process / localization / Endosomal Sorting Complex Required For Transport (ESCRT) / HCMV Late Events / ubiquitin binding / macroautophagy / recycling endosome / positive regulation of protein catabolic process / late endosome membrane / transcription regulator complex / lysosome / endosome membrane / endosome / intracellular membrane-bounded organelle / lipid binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / structural molecule activity / perinuclear region of cytoplasm / protein homodimerization activity / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Im, Y.J. / Hurley, J.H. | ||||||
![]() | ![]() Title: Integrated structural model and membrane targeting mechanism of the human ESCRT-II complex Authors: Im, Y.J. / Hurley, J.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.9 KB | Display | ![]() |
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PDB format | ![]() | 109.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.6 KB | Display | ![]() |
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Full document | ![]() | 489.8 KB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 37.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cuqSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28903.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein | Mass: 26753.189 Da / Num. of mol.: 1 / Fragment: UNP residues 149-386 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Protein | Mass: 12238.329 Da / Num. of mol.: 2 / Fragment: UNP residues 1-102 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.54 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 40% PEG300, 0.1M Tris-HCl, pH8.5, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 19966 / Num. obs: 19408 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Biso Wilson estimate: 100.5 Å2 / Rsym value: 0.047 / Net I/σ(I): 41.3 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.25 / Num. unique all: 1915 / Rsym value: 0.429 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3CUQ Resolution: 2.9→40.74 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.883 / SU B: 46.029 / SU ML: 0.423 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.488 / 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: 90.362 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→40.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 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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