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Yorodumi- PDB-2las: Molecular Determinants of Paralogue-Specific SUMO-SIM Recognition -
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-Basic information
Entry | Database: PDB / ID: 2las | ||||||
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Title | Molecular Determinants of Paralogue-Specific SUMO-SIM Recognition | ||||||
Components |
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Keywords | TRANSCRIPTION / RanBP2 / post-translational modification | ||||||
Function / homology | Function and homology information cytoplasmic periphery of the nuclear pore complex / SUMO ligase activity / SUMO ligase complex / negative regulation of transcription by transcription factor localization / annulate lamellae / SUMOylation of nuclear envelope proteins / 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) ...cytoplasmic periphery of the nuclear pore complex / SUMO ligase activity / SUMO ligase complex / negative regulation of transcription by transcription factor localization / annulate lamellae / SUMOylation of nuclear envelope proteins / 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 / nuclear pore cytoplasmic filaments / small protein activating enzyme binding / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / SUMOylation of DNA methylation proteins / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Maturation of nucleoprotein / Transferases; Acyltransferases; Aminoacyltransferases / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / nuclear export / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / nucleocytoplasmic transport / centrosome localization / Viral Messenger RNA Synthesis / NLS-bearing protein import into nucleus / regulation of gluconeogenesis / negative regulation of protein import into nucleus / ubiquitin-specific protease binding / roof of mouth development / SUMOylation of ubiquitinylation proteins / negative regulation of DNA binding / Vpr-mediated nuclear import of PICs / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / Regulation of HSF1-mediated heat shock response / potassium channel regulator activity / mRNA transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / Regulation of IFNG signaling / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Signaling by ALK fusions and activated point mutants / cellular response to cadmium ion / Resolution of Sister Chromatid Cohesion / response to amphetamine / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / HCMV Late Events / RHO GTPases Activate Formins / positive regulation of protein-containing complex assembly / Transcriptional regulation by small RNAs / SUMOylation of intracellular receptors / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / protein tag activity / ISG15 antiviral mechanism / small GTPase binding / Formation of Incision Complex in GG-NER / HCMV Early Events / Separation of Sister Chromatids / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear envelope / cellular response to heat / snRNP Assembly / nuclear membrane / protein stabilization / nuclear body / nuclear speck / intracellular membrane-bounded organelle / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | closest to the average, model 1 | ||||||
Authors | Namanja, A. / Li, Y. / Su, Y. / Wong, S. / Lu, J. / Colson, L. / Wu, C. / Li, S. / Chen, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Insights into High Affinity Small Ubiquitin-like Modifier (SUMO) Recognition by SUMO-interacting Motifs (SIMs) Revealed by a Combination of NMR and Peptide Array Analysis. Authors: Namanja, A.T. / Li, Y.J. / Su, Y. / Wong, S. / Lu, J. / Colson, L.T. / Wu, C. / Li, S.S. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2las.cif.gz | 326.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2las.ent.gz | 273.3 KB | Display | PDB format |
PDBx/mmJSON format | 2las.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/2las ftp://data.pdbj.org/pub/pdb/validation_reports/la/2las | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11575.005 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OK/SW-cl.43, SMT3C, SMT3H3, SUMO1, UBL1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63165 |
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#2: Protein/peptide | Mass: 1616.852 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49792*PLUS |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
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Sample |
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Sample conditions | Ionic strength: 0 / pH: 6.8 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 200 / Conformers submitted total number: 10 |