+Open data
-Basic information
Entry | Database: PDB / ID: 2vrr | ||||||
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Title | Structure of SUMO modified Ubc9 | ||||||
Components |
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Keywords | CELL CYCLE/LIGASE / E2 / UBC9 / SUMO / LIGASE / NUCLEUS / MITOSIS / MEMBRANE / PHOSPHOPROTEIN / ISOPEPTIDE BOND / CHROMOSOME PARTITION / POSTTRANSLATIONAL MODIFICATION / UBL CONJUGATION PATHWAY / UBIQUITIN LIKE MOLECULE / DEVELOPMENTAL PROTEIN / HOST-VIRUS INTERACTION / CYTOPLASM / CELL CYCLE / MODIFICATION / CELL DIVISION / CELL CYCLE-LIGASE complex | ||||||
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 transcription cofactors / SUMOylation of chromatin organization proteins / SUMOylation of intracellular receptors / SUMOylation of immune response 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 immune response proteins / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of RNA binding proteins / nuclear export / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / ubiquitin-specific protease binding / roof of mouth development / SUMOylation of ubiquitinylation proteins / 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 / Regulation of IFNG signaling / nuclear pore / 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 / SUMOylation of intracellular receptors / protein modification process / 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 / nuclear envelope / cellular response to heat / 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 / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | ||||||
Authors | Knipscheer, P. / Flotho, A. / Klug, H. / Olsen, J.V. / van Dijk, W.J. / Fish, A. / Johnson, E.S. / Mann, M. / Sixma, T.K. / Pichler, A. | ||||||
Citation | Journal: Mol. Cell / Year: 2008 Title: Ubc9 sumoylation regulates SUMO target discrimination. Authors: Knipscheer, P. / Flotho, A. / Klug, H. / Olsen, J.V. / van Dijk, W.J. / Fish, A. / Johnson, E.S. / Mann, M. / Sixma, T.K. / Pichler, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vrr.cif.gz | 116.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vrr.ent.gz | 90.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vrr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/2vrr ftp://data.pdbj.org/pub/pdb/validation_reports/vr/2vrr | 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: 18030.814 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source 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-FMT / #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Sequence details | RESIDUE 20-97 OF SUMO1 PRECEDED BY A START METHIONINE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.9 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 24% (W/V) PEG3350, 200 MM SODIUM FORMATE, 100 MM BIS-TRIS PROPANE PH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 1, 2005 / Details: HELIOS MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→60 Å / Num. obs: 11764 / % possible obs: 97.3 % / Observed criterion σ(I): 1.8 / Redundancy: 12.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.21→2.32 Å / Redundancy: 10 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / % possible all: 81.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1U9B, 2BF8 Resolution: 2.22→61.31 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.874 / SU B: 11.002 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS RESIDUES B94-B96 ARE DISORDERED AND HAVE BEEN GIVEN AN OCCUPANCY OF 0. THERE IS A COVALENT ISOPEPTIDE LINKAGE BETWEEN LYSINE A14 AND GLYCINE B97
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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: 22.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.22→61.31 Å
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