+Open data
-Basic information
Entry | Database: PDB / ID: 7uvc | |||||||||
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Title | Rad6(P43L)-Bre1 Complex | |||||||||
Components |
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Keywords | TRANSFERASE/LIGASE / Rad6 / E2 conjugating enzyme / Bre1 / E3-Ligase / LIGASE / TRANSFERASE-LIGASE complex | |||||||||
Function / homology | Function and homology information MUB1-RAD6-UBR2 ubiquitin ligase complex / RAD6-UBR2 ubiquitin ligase complex / : / Rad6-Rad18 complex / regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / HULC complex / error-free postreplication DNA repair / stress-induced homeostatically regulated protein degradation pathway / ubiquitin-dependent protein catabolic process via the N-end rule pathway ...MUB1-RAD6-UBR2 ubiquitin ligase complex / RAD6-UBR2 ubiquitin ligase complex / : / Rad6-Rad18 complex / regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / HULC complex / error-free postreplication DNA repair / stress-induced homeostatically regulated protein degradation pathway / ubiquitin-dependent protein catabolic process via the N-end rule pathway / meiotic DNA double-strand break formation / cytoplasm protein quality control by the ubiquitin-proteasome system / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / telomere maintenance via recombination / Antigen processing: Ubiquitination & Proteasome degradation / mitotic intra-S DNA damage checkpoint signaling / regulation of DNA-templated DNA replication initiation / DNA duplex unwinding / E2 ubiquitin-conjugating enzyme / sporulation resulting in formation of a cellular spore / error-free translesion synthesis / proteasome binding / ERAD pathway / DNA replication origin binding / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / subtelomeric heterochromatin formation / error-prone translesion synthesis / mitotic G1 DNA damage checkpoint signaling / DNA-templated transcription termination / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / chromosome, telomeric region / protein ubiquitination / DNA repair / chromatin / ATP binding / identical protein binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å | |||||||||
Authors | Shukla, P.K. / Chandrasekharan, M.B. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: Structure and functional determinants of Rad6-Bre1 subunits in the histone H2B ubiquitin-conjugating complex. Authors: Shukla, P.K. / Bissell, J.E. / Kumar, S. / Pokhrel, S. / Palani, S. / Radmall, K.S. / Obidi, O. / Parnell, T.J. / Brasch, J. / Shrieve, D.C. / Chandrasekharan, M.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uvc.cif.gz | 209.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uvc.ent.gz | 169.9 KB | Display | PDB format |
PDBx/mmJSON format | 7uvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/7uvc ftp://data.pdbj.org/pub/pdb/validation_reports/uv/7uvc | HTTPS FTP |
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-Related structure data
Related structure data | 7uv8SC S: Starting model for refinement C: citing same article (ref.) |
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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: 17207.531 Da / Num. of mol.: 1 / Mutation: P43L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: RAD6, UBC2, YGL058W / Plasmid: pRSF-Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P06104, E2 ubiquitin-conjugating enzyme |
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#2: Protein | Mass: 24833.986 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: BRE1, YDL074C / Plasmid: pRSF-Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q07457, RING-type E3 ubiquitin transferase |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.34 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.05 to 0.1 M MMT buffer and 15-25% PEG400 |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2019 / Details: mirror |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→40 Å / Num. obs: 13829 / % possible obs: 99.9 % / Redundancy: 9.7 % / CC1/2: 0.999 / Rsym value: 0.2 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 3.05→3.26 Å / Redundancy: 9.4 % / Num. unique obs: 13829 / CC1/2: 0.674 / Rsym value: 2.79 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7UV8 Resolution: 3.05→37.72 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 37.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 223.7 Å2 / Biso mean: 126.6042 Å2 / Biso min: 67.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.05→37.72 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 273.1186 Å / Origin y: 57.092 Å / Origin z: 125.2036 Å
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Refinement TLS group |
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