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Yorodumi- PDB-2kwu: Solution Structure of UBM2 of murine Polymerase iota in Complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kwu | ||||||
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Title | Solution Structure of UBM2 of murine Polymerase iota in Complex with Ubiquitin | ||||||
Components |
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Keywords | PROTEIN BINDING/SIGNALING PROTEIN / polymerase iota / ubiquitin / ubiquitin-binding motif / UBM / TLS / PROTEIN BINDING-SIGNALING PROTEIN complex | ||||||
Function / homology | Function and homology information Translesion synthesis by POLI / Termination of translesion DNA synthesis / : / : / protein modification process => GO:0036211 / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development ...Translesion synthesis by POLI / Termination of translesion DNA synthesis / : / : / protein modification process => GO:0036211 / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / cellular response to UV-C / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translesion synthesis / cytosolic ribosome / regulation of neuron apoptotic process / energy homeostasis / Regulation of pyruvate metabolism / regulation of proteasomal protein catabolic process / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Josephin domain DUBs / neuron projection morphogenesis / Gap-filling DNA repair synthesis and ligation in GG-NER / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Burschowsky, D. / Rudolf, F. / Rabut, G. / Herrmann, T. / Peter, M. / Wider, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural analysis of the conserved ubiquitin-binding motifs (UBMs) of the translesion polymerase iota in complex with ubiquitin. Authors: Burschowsky, D. / Rudolf, F. / Rabut, G. / Herrmann, T. / Matthias, P. / Wider, G. | ||||||
History |
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Remark 650 | HELIX: DETERMINATION METHOD: AUTHOR | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kwu.cif.gz | 701.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kwu.ent.gz | 584.8 KB | Display | PDB format |
PDBx/mmJSON format | 2kwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kwu_validation.pdf.gz | 367.2 KB | Display | wwPDB validaton report |
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Full document | 2kwu_full_validation.pdf.gz | 578.5 KB | Display | |
Data in XML | 2kwu_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 2kwu_validation.cif.gz | 58.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/2kwu ftp://data.pdbj.org/pub/pdb/validation_reports/kw/2kwu | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 5704.247 Da / Num. of mol.: 1 Fragment: C-terminal ubiquitin-binding motif (UNP residues 673-717) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Poli, Rad30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star DE3 / References: UniProt: Q6R3M4 |
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#2: Protein | Mass: 8576.831 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star DE3 / References: UniProt: P62988, UniProt: P0CG47*PLUS |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.189 / pH: 6.0 / Pressure: ambient / Temperature: 288 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 2758 / NOE intraresidue total count: 672 / NOE long range total count: 548 / NOE medium range total count: 778 / NOE sequential total count: 760 | ||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |