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Open data
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Basic information
Entry | Database: PDB / ID: 6op8 | |||||||||||||||
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Title | S. pombe Ubc7/U7BR complex | |||||||||||||||
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![]() | LIGASE/PROTEIN BINDING / UBL CONJUGATION PATHWAY / ENDOPLASMIC RETICULUM-ASSOCIATED DEGRADATION / LIGASE / LIGASE-PROTEIN BINDING complex | |||||||||||||||
Function / homology | ![]() negative regulation of transcription by transcription factor catabolism / Hrd1p ubiquitin ligase complex / : / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-protein transferase activator activity / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ubiquitin binding / protein polyubiquitination ...negative regulation of transcription by transcription factor catabolism / Hrd1p ubiquitin ligase complex / : / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-protein transferase activator activity / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ubiquitin binding / protein polyubiquitination / ubiquitin-dependent protein catabolic process / endoplasmic reticulum / mitochondrion / ATP binding / nucleus / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Hann, Z.S. / Lima, C.D. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the Schizosaccharomyces pombe U7BR E2-binding region in complex with Ubc7. Authors: Hann, Z.S. / Metzger, M.B. / Weissman, A.M. / Lima, C.D. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.7 KB | Display | ![]() |
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PDB format | ![]() | 45.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 262.4 KB | Display | ![]() |
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Full document | ![]() | 262.3 KB | Display | |
Data in XML | ![]() | 1.2 KB | Display | |
Data in CIF | ![]() | 4.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jquS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 19206.811 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: ubc7, ubcp3, SPBP16F5.04 / Plasmid: pET29b / Production host: ![]() ![]() References: UniProt: O00102, E2 ubiquitin-conjugating enzyme |
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#2: Protein | Mass: 7814.836 Da / Num. of mol.: 1 / Fragment: residues 152-215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: SPCC4G3.13c / Plasmid: pET28b / Production host: ![]() ![]() |
-Non-polymers , 4 types, 217 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM TRIS, pH 8.0, 200 mM MgCl2, 30% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.703→47.2787 Å / Num. obs: 22673 / % possible obs: 99.39 % / Redundancy: 5.7 % / Biso Wilson estimate: 14.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0562 / Rpim(I) all: 0.02523 / Rrim(I) all: 0.06177 / Net I/σ(I): 25.94 |
Reflection shell | Resolution: 1.703→1.764 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.2232 / Mean I/σ(I) obs: 9.05 / Num. unique obs: 2195 / CC1/2: 0.97 / Rpim(I) all: 0.1023 / Rrim(I) all: 0.2461 / % possible all: 98.12 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JQU Resolution: 1.703→47.26 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.47 Å2 / Biso mean: 20.4469 Å2 / Biso min: 3.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.703→47.26 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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