+Open data
-Basic information
Entry | Database: PDB / ID: 6do5 | ||||||
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Title | KLHDC2 ubiquitin ligase in complex with USP1 C-end degron | ||||||
Components |
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Keywords | LIGASE / kelch repeat / beta-propeller / degron / complex / substrate receptor / E3 / ubiquitin ligase | ||||||
Function / homology | Function and homology information positive regulation of error-prone translesion synthesis / monoubiquitinated protein deubiquitination / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / protein deubiquitination / ubiquitin ligase-substrate adaptor activity / regulation of DNA repair / response to UV / skeletal system development / Recognition of DNA damage by PCNA-containing replication complex ...positive regulation of error-prone translesion synthesis / monoubiquitinated protein deubiquitination / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / protein deubiquitination / ubiquitin ligase-substrate adaptor activity / regulation of DNA repair / response to UV / skeletal system development / Recognition of DNA damage by PCNA-containing replication complex / Fanconi Anemia Pathway / positive regulation of receptor signaling pathway via JAK-STAT / peptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear membrane / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / protein ubiquitination / cysteine-type endopeptidase activity / DNA repair / proteolysis / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Rusnac, D.V. / Lin, H.C. / Yen, H.C.S. / Zheng, N. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mol. Cell / Year: 2018 Title: Recognition of the Diglycine C-End Degron by CRL2KLHDC2Ubiquitin Ligase. Authors: Rusnac, D.V. / Lin, H.C. / Canzani, D. / Tien, K.X. / Hinds, T.R. / Tsue, A.F. / Bush, M.F. / Yen, H.S. / Zheng, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6do5.cif.gz | 143.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6do5.ent.gz | 109.5 KB | Display | PDB format |
PDBx/mmJSON format | 6do5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/6do5 ftp://data.pdbj.org/pub/pdb/validation_reports/do/6do5 | HTTPS FTP |
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-Related structure data
Related structure data | 6do3C 6do4C 2vpjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41351.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLHDC2, HCA33 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y2U9 #2: Protein/peptide | Mass: 528.644 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O94782*PLUS #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.93 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop Details: 0.03M MgCl2*6H2O, 0.03M CaCl2*2H2O, 0.05M Imidazole, 0.05M MES monohydrate, 12.5% v/v MPD, 12.5% PEG1000, 12.5% w/v PEG3350, pH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. obs: 32634 / % possible obs: 98 % / Redundancy: 5.9 % / Biso Wilson estimate: 32.82 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.053 / Rrim(I) all: 0.13 / Χ2: 1.236 / Net I/σ(I): 6.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VPJ Resolution: 2.5→43.067 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.87
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.12 Å2 / Biso mean: 32.64 Å2 / Biso min: 15.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→43.067 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %
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