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Yorodumi- PDB-2khw: Solution Structure of the human Polymerase iota UBM2-Ubiquitin Complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 2khw | ||||||
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Title | Solution Structure of the human Polymerase iota UBM2-Ubiquitin Complex | ||||||
Components |
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Keywords | Transferase/protein binding / UBM / ubiquitin-binding domain / polymerase iota / translesion synthesis / TLS / Cytoplasm / Nucleus / protein binding / transcription regulator activity / Transferase-protein binding COMPLEX | ||||||
Function / homology | Function and homology information : / : / protein modification process => GO:0036211 / hypothalamus gonadotrophin-releasing hormone neuron development / IgG binding / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development ...: / : / protein modification process => GO:0036211 / hypothalamus gonadotrophin-releasing hormone neuron development / IgG binding / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / translesion synthesis / error-prone translesion synthesis / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / regulation of proteasomal protein catabolic process / energy homeostasis / regulation of neuron apoptotic process / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / cytosolic ribosome / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / 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 / neuron projection morphogenesis / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of mitochondrial membrane potential / 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 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway Similarity search - Function | ||||||
Biological species | Streptococcus sp. (bacteria) Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Bomar, M.G. / D'Souza, S. / Bienko, M. / Dikic, I. / Walker, G. | ||||||
Citation | Journal: To be Published Title: Solution Structure of the human Polymerase iota UBM2-Ubiquitin Complex Authors: Bomar, M.G. / D'Souza, S. / Bienko, M. / Dikic, I. / Walker, G. / Zhou, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2khw.cif.gz | 844.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2khw.ent.gz | 730.1 KB | Display | PDB format |
PDBx/mmJSON format | 2khw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/2khw ftp://data.pdbj.org/pub/pdb/validation_reports/kh/2khw | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Antibody | Mass: 12348.556 Da / Num. of mol.: 1 / Fragment: UNP residues 304-357, 676-715 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sp., Homo sapiens / Gene: spg, POLI, RAD30B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P19909, UniProt: Q9UNA4, DNA-directed DNA polymerase |
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#2: Protein | Mass: 8859.106 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(DE3) / References: UniProt: P62988, UniProt: P0CG47*PLUS |
Sequence details | ACCORDING TO THE AUTHORS THE N-TERMINAL PART IS A GB1 TAG USED FOR ENHANCEMENT OF PROTEIN ...ACCORDING TO THE AUTHORS THE N-TERMINAL PART IS A GB1 TAG USED FOR ENHANCEMEN |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Solution Structure of the human Polymerase iota UBM2-Ubiquitin Complex | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 40 / Conformers submitted total number: 25 |