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Yorodumi- PDB-6cwy: Crystal structure of SUMO E1 in complex with an allosteric inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cwy | ||||||
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Title | Crystal structure of SUMO E1 in complex with an allosteric inhibitor | ||||||
Components | (SUMO-activating enzyme subunit ...) x 2 | ||||||
Keywords | transferase/transferase inhibitor / ROSSMANN-LIKE FOLD / UBIQUITIN-LIKE FOLD / UBIQUITIN ACTIVATING ENZYME / ACTIVITY / ATP BINDING / LIGASE ACTIVITY / ATP/MG BINDING / UBIQUITIN E2 / LIGASE / TRANSFERASE / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information SUMO activating enzyme complex / SUMO activating enzyme activity / ubiquitin activating enzyme activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO binding / small protein activating enzyme binding / positive regulation of protein sumoylation / ATP-dependent protein binding / Transferases; Acyltransferases; Aminoacyltransferases ...SUMO activating enzyme complex / SUMO activating enzyme activity / ubiquitin activating enzyme activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO binding / small protein activating enzyme binding / positive regulation of protein sumoylation / ATP-dependent protein binding / Transferases; Acyltransferases; Aminoacyltransferases / ubiquitin-like protein conjugating enzyme binding / positive regulation of protein targeting to mitochondrion / protein sumoylation / enzyme activator activity / transferase activity / protein heterodimerization activity / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.462 Å | ||||||
Authors | Lv, Z. / Yuan, L. / Atkison, J.H. / Williams, K.M. / Olsen, S.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Molecular mechanism of a covalent allosteric inhibitor of SUMO E1 activating enzyme. Authors: Lv, Z. / Yuan, L. / Atkison, J.H. / Williams, K.M. / Vega, R. / Sessions, E.H. / Divlianska, D.B. / Davies, C. / Chen, Y. / Olsen, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cwy.cif.gz | 333.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cwy.ent.gz | 270.3 KB | Display | PDB format |
PDBx/mmJSON format | 6cwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/6cwy ftp://data.pdbj.org/pub/pdb/validation_reports/cw/6cwy | HTTPS FTP |
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-Related structure data
Related structure data | 6cwzC 3kycS 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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Unit cell |
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-Components
-SUMO-activating enzyme subunit ... , 2 types, 2 molecules CD
#1: Protein | Mass: 38499.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SAE1, AOS1, SUA1, UBLE1A / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Codon Plus / References: UniProt: Q9UBE0 |
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#2: Protein | Mass: 73485.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBA2, SAE2, UBLE1B, HRIHFB2115 / Plasmid: PET-28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 codon plus References: UniProt: Q9UBT2, Transferases; Acyltransferases; Aminoacyltransferases |
-Non-polymers , 6 types, 54 molecules
#3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-FHJ / | #8: 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: 2.53 Å3/Da / Density % sol: 51.36 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M ammonium sulfate, 0.1M Bis-Tris HCl pH 6.5, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→50 Å / Num. obs: 41866 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 53.48 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.042 / Rrim(I) all: 0.098 / Χ2: 0.619 / Net I/σ(I): 5.5 / Num. measured all: 216502 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KYC Resolution: 2.462→48.284 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.9 / 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: 206.5 Å2 / Biso mean: 75.9999 Å2 / Biso min: 27.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.462→48.284 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: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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