+Open data
-Basic information
Entry | Database: PDB / ID: 2uyz | ||||||
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Title | Non-covalent complex between Ubc9 and SUMO1 | ||||||
Components |
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Keywords | LIGASE / SUMOYLATION / CELL DIVISION / NUCLEAR PROTEIN / UBIQUITIN-LIKE MODIFIER / UBL CONJUGATION PATHWAY / CONJUGATING ENZYME / CHROMOSOME PARTITION / E2 / UBC9 / SUMO1 / MITOSIS / CELL CYCLE | ||||||
Function / homology | Function and homology information SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMOylation of nuclear envelope proteins / Vitamin D (calciferol) metabolism / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of ubiquitinylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins ...SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMOylation of nuclear envelope proteins / Vitamin D (calciferol) metabolism / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of ubiquitinylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA methylation proteins / SUMOylation of DNA damage response and repair proteins / SUMOylation of intracellular receptors / SUMOylation of immune response proteins / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / Processing of DNA double-strand break ends / HLH domain binding / SUMO conjugating enzyme activity / Formation of Incision Complex in GG-NER / RING-like zinc finger domain binding / SUMO ligase complex / negative regulation of transcription by transcription factor localization / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of nuclear envelope proteins / bHLH transcription factor binding / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of immune response proteins / nuclear export / Maturation of nucleoprotein / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of RNA binding proteins / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / ubiquitin-specific protease binding / SUMOylation of ubiquitinylation proteins / roof of mouth development / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / potassium channel regulator activity / SUMOylation of DNA damage response and repair proteins / nuclear pore / Regulation of IFNG signaling / cellular response to cadmium ion / ionotropic glutamate receptor binding / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / chromosome segregation / transcription coregulator binding / positive regulation of protein-containing complex assembly / protein modification process / SUMOylation of intracellular receptors / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / protein tag activity / fibrillar center / Formation of Incision Complex in GG-NER / ubiquitin-protein transferase activity / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / nuclear envelope / positive regulation of canonical NF-kappaB signal transduction / nuclear membrane / protein stabilization / nuclear body / positive regulation of cell migration / nuclear speck / cell division / DNA repair / negative regulation of DNA-templated transcription / dendrite / ubiquitin protein ligase binding / nucleolus / negative regulation of transcription by RNA polymerase II / enzyme binding / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Knipscheer, P. / van Dijk, W.J. / Olsen, J.V. / Mann, M. / Sixma, T.K. | ||||||
Citation | Journal: EMBO J. / Year: 2007 Title: Noncovalent interaction between Ubc9 and SUMO promotes SUMO chain formation. Authors: Knipscheer, P. / van Dijk, W.J. / Olsen, J.V. / Mann, M. / Sixma, T.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uyz.cif.gz | 134.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uyz.ent.gz | 105.2 KB | Display | PDB format |
PDBx/mmJSON format | 2uyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/2uyz ftp://data.pdbj.org/pub/pdb/validation_reports/uy/2uyz | HTTPS FTP |
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-Related 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: 18014.750 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: START METHIONINE (1) AND SECOND SERINE (2) ARE MISSING IN STRUCTURE Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63280, ubiquitin-protein ligase | ||
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#2: Protein | Mass: 9230.559 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-97 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63165 | ||
#3: Chemical | ChemComp-NA / | ||
#4: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | C93S MUTANT | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43 % |
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Crystal grow | pH: 5.5 Details: 16.5 % (W/V) PEG3350 100 MM BISTRIS PH 5.5 15 % (W/V) GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 18, 2007 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→40 Å / Num. obs: 49557 / % possible obs: 99.2 % / Observed criterion σ(I): 1.5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 1.6 / % possible all: 99.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1U9A, 2BF8 Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.668 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→50 Å
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