+Open data
-Basic information
Entry | Database: PDB / ID: 1u9b | ||||||
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Title | MURINE/HUMAN UBIQUITIN-CONJUGATING ENZYME UBC9 | ||||||
Components | UBIQUITIN-CONJUGATING ENZYME E9 | ||||||
Keywords | LIGASE / UBIQUITIN-CONJUGATING ENZYME / UBIQUITIN-DIRECTED PROTEOLYSIS / CELL CYCLE CONTROL | ||||||
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 / HLH domain binding / SUMO conjugating enzyme activity / Formation of Incision Complex in GG-NER / Processing of DNA double-strand break ends / SUMO ligase complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / bHLH transcription factor binding / Transferases; Acyltransferases; Aminoacyltransferases / presynaptic cytosol / nuclear export / SUMO transferase activity / postsynaptic cytosol / protein sumoylation / nuclear pore / ionotropic glutamate receptor binding / chromosome segregation / modulation of chemical synaptic transmission / protein modification process / Schaffer collateral - CA1 synapse / fibrillar center / ubiquitin-protein transferase activity / nuclear envelope / positive regulation of canonical NF-kappaB signal transduction / nuclear body / cell division / glutamatergic synapse / dendrite / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Tong, H. / Hateboer, G. / Perrakis, A. / Bernards, R. / Sixma, T.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1997 Title: Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system. Authors: Tong, H. / Hateboer, G. / Perrakis, A. / Bernards, R. / 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 | 1u9b.cif.gz | 45.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u9b.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 1u9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1u9b_validation.pdf.gz | 421.2 KB | Display | wwPDB validaton report |
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Full document | 1u9b_full_validation.pdf.gz | 425.6 KB | Display | |
Data in XML | 1u9b_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 1u9b_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/1u9b ftp://data.pdbj.org/pub/pdb/validation_reports/u9/1u9b | HTTPS FTP |
-Related structure data
Related structure data | 1u9aC 1aak 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
#1: Protein | Mass: 18258.076 Da / Num. of mol.: 1 / Mutation: INS(ASN 0) Source method: isolated from a genetically manipulated source Details: MAMMALIAN / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P63280, ubiquitin-protein ligase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 23% PEG MONOMETHYL ETHER 5000,9% ISOPROPANOL, 0.1 M AMMONIUM SULFATE, 0.1 M MES BUFFER, PH6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 281 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.885 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 26, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.885 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 12854 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.02→2.05 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3 / Rsym value: 0.41 / % possible all: 99 |
Reflection shell | *PLUS % possible obs: 99 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AAK 1aak Resolution: 2→10 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 228.3 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5D / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.185 / Rfactor Rfree: 0.252 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 26.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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