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Yorodumi- PDB-7p47: Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p47 | ||||||
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Title | Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO thioester mimetic | ||||||
Components |
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Keywords | LIGASE / SUMO E3 ligase activity / DNA repair | ||||||
Function / homology | Function and homology information Smc5-Smc6 complex / resolution of DNA recombination intermediates / SUMO conjugating enzyme activity / DNA double-strand break attachment to nuclear envelope / chromosome separation / SUMO ligase activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins ...Smc5-Smc6 complex / resolution of DNA recombination intermediates / SUMO conjugating enzyme activity / DNA double-strand break attachment to nuclear envelope / chromosome separation / SUMO ligase activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins / SUMO is proteolytically processed / mitotic spindle elongation / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / SUMOylation of chromatin organization proteins / chromatin looping / protein serine/threonine kinase inhibitor activity / Transferases; Acyltransferases; Aminoacyltransferases / recombinational repair / regulation of telomere maintenance / SUMO transferase activity / ubiquitin-like protein ligase binding / protein sumoylation / condensed nuclear chromosome / double-strand break repair via homologous recombination / protein tag activity / single-stranded DNA binding / nuclear envelope / chromosome, telomeric region / damaged DNA binding / cell division / DNA repair / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.314 Å | ||||||
Authors | Lascorz, J. / Varejao, N. / Reverter, D. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis for the E3 ligase activity enhancement of yeast Nse2 by SUMO-interacting motifs. Authors: Varejao, N. / Lascorz, J. / Codina-Fabra, J. / Belli, G. / Borras-Gas, H. / Torres-Rosell, J. / Reverter, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p47.cif.gz | 244.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p47.ent.gz | 195.3 KB | Display | PDB format |
PDBx/mmJSON format | 7p47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/7p47 ftp://data.pdbj.org/pub/pdb/validation_reports/p4/7p47 | HTTPS FTP |
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-Related structure data
Related structure data | 3htkS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9978.620 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SMC5, YOL034W / Production host: Escherichia coli (E. coli) / References: UniProt: Q08204 | ||||
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#2: Protein | Mass: 19071.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Point mutants A129K, K153R Isopeptidic bond between K129 (chain A) and G98 (chain D) Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: UBC9, YDL064W / Production host: Escherichia coli (E. coli) References: UniProt: P50623, Transferases; Acyltransferases; Aminoacyltransferases | ||||
#3: Protein | Mass: 24117.096 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: MMS21, NSE2, YEL019C / Production host: Escherichia coli (E. coli) References: UniProt: P38632, Transferases; Acyltransferases; Aminoacyltransferases | ||||
#4: Protein | Mass: 13739.396 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SMT3, YDR510W, D9719.15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12306 #5: Chemical | ChemComp-ZN / | 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: 2.78 Å3/Da / Density % sol: 55.75 % |
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Crystal grow | Temperature: 311 K / Method: vapor diffusion, hanging drop Details: 12% PEG8000, 0.2M dimethyl-2-hydroxyethylammoniumpropane sulfonate (NDSB 211), 8% ethylene glycol, 0.1M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.31→47.14 Å / Num. obs: 13097 / % possible obs: 99.2 % / Redundancy: 5.4 % / CC1/2: 0.99 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 3.31→3.58 Å / Num. unique obs: 2585 / CC1/2: 0.68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HTK Resolution: 3.314→47.135 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.58 / 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: 198.58 Å2 / Biso mean: 98.82 Å2 / Biso min: 57.74 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.314→47.135 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 19.2457 Å / Origin y: -12.4467 Å / Origin z: -20.4649 Å
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Refinement TLS group |
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