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Open data
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Basic information
Entry | Database: PDB / ID: 2caz | ||||||
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Title | ESCRT-I core | ||||||
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![]() | PROTEIN TRANSPORT / ESCRT / MVB / MULTIVESICULAR BODIES / ENDOSOME / LYSOSOME / PH DOMAIN / PROTEIN SORTING / VESICLE TRAFFICKING / UBIQUITIN / PHOSPHOINOSITIDE / PTDINS3P / VPS23 / VPS28 / VPS37 / VPS36 / COILED COIL / UBL CONJUGATION PATHWAY | ||||||
Function / homology | ![]() negative regulation of protein polyubiquitination / ESCRT I complex / ATP export / Endosomal Sorting Complex Required For Transport (ESCRT) / endosome transport via multivesicular body sorting pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to vacuole / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to membrane ...negative regulation of protein polyubiquitination / ESCRT I complex / ATP export / Endosomal Sorting Complex Required For Transport (ESCRT) / endosome transport via multivesicular body sorting pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to vacuole / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to membrane / reticulophagy / endosome to lysosome transport / ubiquitin binding / protein modification process / cytoplasmic side of plasma membrane / late endosome membrane / endosome / protein-containing complex binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gill, D.J. / Teo, H. / Sun, J. / Perisic, O. / Veprintsev, D.B. / Vallis, Y. / Emr, S.D. / Williams, R.L. | ||||||
![]() | ![]() Title: Escrt-I Core and Escrt-II Glue Domain Structures Reveal Role for Glue in Linking to Escrt-I and Membranes. Authors: Teo, H. / Gill, D.J. / Sun, J. / Perisic, O. / Veprintsev, D.B. / Wallis, Y. / Emr, S.D. / Williams, R.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.4 KB | Display | ![]() |
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PDB format | ![]() | 69 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.8 KB | Display | ![]() |
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Full document | ![]() | 492.8 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 9353.570 Da / Num. of mol.: 2 / Fragment: RESIDUES 305-385 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: POPCH / Production host: ![]() ![]() #2: Protein | Mass: 17763.697 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: POPCH / Production host: ![]() ![]() #3: Protein | Mass: 10213.293 Da / Num. of mol.: 2 / Fragment: RESIDUES 130-213 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: POPCH / Production host: ![]() ![]() Compound details | THE ESCRT-I COMPLEX RECOGNIZES UBIQUITINATED MULTIVESICULAR BODY (MVB) CARGO. REQUIRED FOR NORMAL ...THE ESCRT-I COMPLEX RECOGNIZES | Sequence details | RESIDUES 305-385 RESIDUES 1-147 WITH N-TERMINAL MAHHHHHH AFFINITY TAG RESIDUES 130-213 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 290 K / pH: 7 Details: 8-10% PEG 8000, 8-9% ETHYLENE GLYCOL, 0.1 M HEPES (PH 7.0- 8.0), 17 DEG C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 6, 2005 / Details: TORROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→43 Å / Num. obs: 9610 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.21 |
Reflection shell | Resolution: 3.6→3.8 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 1.8 Å / VDW probe radii: 1.8 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.5 Å2
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Refinement step | Cycle: LAST / Resolution: 3.6→145.86 Å
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Refine LS restraints |
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