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- PDB-2khw: Solution Structure of the human Polymerase iota UBM2-Ubiquitin Complex -

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Basic information

Entry
Database: PDB / ID: 2khw
TitleSolution Structure of the human Polymerase iota UBM2-Ubiquitin Complex
Components
  • Immunoglobulin G-binding protein G, DNA polymerase iota
  • Ubiquitin
KeywordsTransferase/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 / fat pad development / mitochondrion transport along microtubule / female gonad development ...: / : / protein modification process => GO:0036211 / hypothalamus gonadotrophin-releasing hormone neuron development / IgG binding / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / error-prone translesion synthesis / Major pathway of rRNA processing in the nucleolus and cytosol / translesion synthesis / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / cytosolic ribosome / 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) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / neuron projection morphogenesis / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / regulation of mitochondrial membrane potential / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling
Similarity search - Function
HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily ...HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Roll / DNA/RNA polymerase superfamily / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / Immunoglobulin G-binding protein G / Ubiquitin-60S ribosomal protein L40 / DNA polymerase iota
Similarity search - Component
Biological speciesStreptococcus sp. (bacteria)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBomar, M.G. / D'Souza, S. / Bienko, M. / Dikic, I. / Walker, G.
CitationJournal: 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
DepositionApr 13, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G, DNA polymerase iota
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)21,2082
Polymers21,2082
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Antibody Immunoglobulin G-binding protein G, DNA polymerase iota / IgG-binding protein G / RAD30 homolog B / Eta2


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
#2: Protein Ubiquitin


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 detailsACCORDING 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 ENHANCEMENT OF PROTEIN SOLUBILITY. THEY CHOSE TO DEPOSIT ONLY THE C-TERMINAL PART OF THE SEQUENCE CORRESPONDING TO DNA POLYMERASE IOTA. THESE 2 SEGMENTS ARE LINKED BY THE RESIDUES GSDE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution Structure of the human Polymerase iota UBM2-Ubiquitin Complex
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2123D HNCO
2223D HNCA
2323D HN(CA)CB
2423D HN(CO)CA
2523D HN(COCA)CB
3633D (H)CCH-TOCSY
2723D 1H-15N NOESY
3833D 1H-13C NOESY
1913D 1H-15N NOESY
41043D 1H-13C NOESY
41143D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] entity_1-1, 4 mM entity_2-2, 90% H2O/10% D2O90% H2O/10% D2O
23 mM [U-100% 15N] entity_1-3, 3 mM [U-100% 15N] entity_2-4, 90% H2O/10% D2O90% H2O/10% D2O
33 mM [U-100% 13C; U-100% 15N] entity_1-5, 3 mM [U-100% 13C; U-100% 15N] entity_2-6, 100% D2O100% D2O
41 mM [U-100% 13C; U-100% 15N] entity_1-7, 4 mM entity_2-8, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity_1-1[U-100% 15N]1
4 mMentity_2-21
3 mMentity_1-3[U-100% 15N]2
3 mMentity_2-4[U-100% 15N]2
3 mMentity_1-5[U-100% 13C; U-100% 15N]3
3 mMentity_2-6[U-100% 13C; U-100% 15N]3
1 mMentity_1-7[U-100% 13C; U-100% 15N]4
4 mMentity_2-84
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11007ambient 298 K
21007ambient 298 K
31007ambient 298 K
41007ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 25

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