+Open data
-Basic information
Entry | Database: PDB / ID: 1u9a | ||||||
---|---|---|---|---|---|---|---|
Title | HUMAN UBIQUITIN-CONJUGATING ENZYME UBC9 | ||||||
Components | UBIQUITIN-CONJUGATING ENZYME | ||||||
Keywords | UBIQUITIN-CONJUGATING ENZYME / UBIQUITIN-DIRECTED PROTEOLYSIS / CELL CYCLE CONTROL / LIGASE | ||||||
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 / presynaptic cytosol / nuclear export / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / postsynaptic cytosol / protein sumoylation / nuclear pore / ionotropic glutamate receptor binding / chromosome segregation / protein modification process / modulation of chemical synaptic transmission / 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 / cytoplasm / cytosol 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1u9a.cif.gz | 46.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1u9a.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 1u9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1u9a_validation.pdf.gz | 392.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1u9a_full_validation.pdf.gz | 397.3 KB | Display | |
Data in XML | 1u9a_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 1u9a_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/1u9a ftp://data.pdbj.org/pub/pdb/validation_reports/u9/1u9a | HTTPS FTP |
-Related structure data
Related structure data | 1u9bC 1aak S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18258.076 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P63280, ubiquitin-protein ligase |
---|---|
#2: Water | ChemComp-HOH / |
Sequence details | RESIDUES WITH RESIDUE NUMBERS BELOW 1 ARE CLONING ARTIFACTS. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED IN THE SPACE GROUP P21 FROM 9% PEG 4000, 9% ISOPROPANOL, 0.1 M HEPES, PH 7.5 SYMMETRY OPERATIONS FOR NON-STANDARD SETTING: P 21: X, Y,Z -X,Y+1/2,-Z | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 281 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / 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: 12295 / % possible obs: 91 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.42 / % possible all: 94 |
Reflection shell | *PLUS % possible obs: 94 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: BABINET SCALING / Bsol: 259.4 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.16 / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|