+Open data
-Basic information
Entry | Database: PDB / ID: 3a4s | ||||||
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Title | The crystal structure of the SLD2:Ubc9 complex | ||||||
Components |
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Keywords | LIGASE/TRNASCRIPTION / ubiquitin fold / SUMO / Coiled coil / Cytoplasm / Methylation / Nucleus / ATP-binding / Cell cycle / Cell division / Chromosome partition / Host-virus interaction / Isopeptide bond / Ligase / Mitosis / Nucleotide-binding / Ubl conjugation / Ubl conjugation pathway / LIGASE-TRNASCRIPTION COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / mitotic nuclear membrane reassembly / Vitamin D (calciferol) metabolism ...positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / mitotic nuclear membrane reassembly / Vitamin D (calciferol) metabolism / synaptonemal complex / 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 / SUMOylation of ubiquitinylation proteins / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / SUMOylation of DNA damage response and repair proteins / nuclear pore / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Meiotic synapsis / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / chromosome segregation / transcription coregulator binding / protein modification process / SUMOylation of intracellular receptors / PKR-mediated signaling / PML body / Formation of Incision Complex in GG-NER / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear envelope / Processing of DNA double-strand break ends / ubiquitin-dependent protein catabolic process / positive regulation of cell migration / cell division / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Sekiyama, N. / Arita, K. / Ikeda, Y. / Ariyoshi, M. / Tochio, H. / Saitoh, H. / Shirakawa, M. | ||||||
Citation | Journal: Proteins / Year: 2009 Title: Structural basis for regulation of poly-SUMO chain by a SUMO-like domain of Nip45 Authors: Sekiyama, N. / Arita, K. / Ikeda, Y. / Hashiguchi, K. / Ariyoshi, M. / Tochio, H. / Saitoh, H. / Shirakawa, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a4s.cif.gz | 99.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a4s.ent.gz | 76.9 KB | Display | PDB format |
PDBx/mmJSON format | 3a4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/3a4s ftp://data.pdbj.org/pub/pdb/validation_reports/a4/3a4s | HTTPS FTP |
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-Related structure data
Related structure data | 3a4rSC 1a3sS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 18442.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Ubc9 / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P63279, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Protein | Mass: 8677.913 Da / Num. of mol.: 2 / Fragment: SLD2, Ubiquitin-like domain, residues 339-412 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nip45 / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O09130 Sequence details | THIS COORDINATE | |
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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: 2.49 Å3/Da / Density % sol: 50.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 25% polyethylene glycol 1500, 0.1M SPG buffer : SPG buffer was prepared by mixing succinic acid, sodium dihydrogen phosphate, and glycine in the molar ratios 2:7:7, pH 6.0, VAPOR DIFFUSION, ...Details: 25% polyethylene glycol 1500, 0.1M SPG buffer : SPG buffer was prepared by mixing succinic acid, sodium dihydrogen phosphate, and glycine in the molar ratios 2:7:7, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→46.4 Å / Num. obs: 13920 / % possible obs: 93.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 38.93 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 18.2 / Num. measured all: 645440 |
Reflection shell | Resolution: 2.58→2.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.196 / % possible all: 73.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries; 1A3S and 3A4R Resolution: 2.7→46.366 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.776 / SU ML: 0.41 / σ(F): 1.98 / Phase error: 29.46 / 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 / Bsol: 20.944 Å2 / ksol: 0.335 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.02 Å2 / Biso mean: 42.69 Å2 / Biso min: 11.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→46.366 Å
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Refine LS restraints |
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LS refinement shell |
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