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Yorodumi- PDB-7uw7: Crystal structure of the Human TRIP12 WWE domain (isoform 2) in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uw7 | ||||||
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Title | Crystal structure of the Human TRIP12 WWE domain (isoform 2) in complex with ADP | ||||||
Components | Isoform 2 of E3 ubiquitin-protein ligase TRIP12 | ||||||
Keywords | LIGASE / TRIP12 / WWE / Isoform 2 / SGC / Structural Genomics / Structural Genomics Consortium | ||||||
Function / homology | Function and homology information : / negative regulation of double-strand break repair / regulation of double-strand break repair / HECT-type E3 ubiquitin transferase / nuclear thyroid hormone receptor binding / regulation of embryonic development / protein polyubiquitination / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process ...: / negative regulation of double-strand break repair / regulation of double-strand break repair / HECT-type E3 ubiquitin transferase / nuclear thyroid hormone receptor binding / regulation of embryonic development / protein polyubiquitination / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / nuclear speck / DNA repair / DNA damage response / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å | ||||||
Authors | Kimani, S. / Dong, A. / Li, Y. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC) | ||||||
Funding support | Canada, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the Human TRIP12 WWE domain (isoform 2) in complex with ADP Authors: Kimani, S. / Dong, A. / Li, Y. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uw7.cif.gz | 34.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uw7.ent.gz | 19.8 KB | Display | PDB format |
PDBx/mmJSON format | 7uw7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/7uw7 ftp://data.pdbj.org/pub/pdb/validation_reports/uw/7uw7 | HTTPS FTP |
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-Related structure data
Related structure data | 6miwS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9090.911 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRIP12, KIAA0045, ULF / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta References: UniProt: Q14669-2, HECT-type E3 ubiquitin transferase | ||||
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#2: Chemical | ChemComp-ADP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.15 % / Mosaicity: 0.13 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350, 0.1 M Sodium Hepes, MOPS pH 7.5, 0.09 M Sodium nitrate, 0.09 M Sodium phosphate dibasic, 0.09 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2022 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.17→50 Å / Num. obs: 23321 / % possible obs: 98.3 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Χ2: 1.187 / Net I/σ(I): 11.5 / Num. measured all: 153097 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MIW Resolution: 1.17→30.05 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.601 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 36.98 Å2 / Biso mean: 10.821 Å2 / Biso min: 4.84 Å2
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Refinement step | Cycle: final / Resolution: 1.17→30.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.17→1.2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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