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- PDB-2kwv: Solution Structure of UBM1 of murine Polymerase iota in Complex w... -

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Basic information

Entry
Database: PDB / ID: 2kwv
TitleSolution Structure of UBM1 of murine Polymerase iota in Complex with Ubiquitin
Components
  • DNA polymerase iota
  • Ubiquitin
KeywordsPROTEIN 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 / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / Peptide chain elongation / Selenocysteine synthesis ...Translesion synthesis by POLI / Termination of translesion DNA synthesis / : / : / protein modification process => GO:0036211 / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / cellular response to UV-C / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Maturation of protein E / Maturation of protein E / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / L13a-mediated translational silencing of Ceruloplasmin expression / 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) / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / translesion synthesis / Major pathway of rRNA processing in the nucleolus and cytosol / 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 induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of activated PAK-2p34 by proteasome mediated degradation / TNFR1-induced NF-kappa-B signaling pathway / PINK1-PRKN Mediated Mitophagy / cytosolic ribosome / TCF dependent signaling in response to WNT / Autodegradation of Cdh1 by Cdh1:APC/C / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / APC/C:Cdc20 mediated degradation of Securin / activated TAK1 mediates p38 MAPK activation / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / Regulation of signaling by CBL / NIK-->noncanonical NF-kB signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / SCF-beta-TrCP mediated degradation of Emi1 / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / TNFR2 non-canonical NF-kB pathway / Negative regulation of FGFR3 signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Fanconi Anemia Pathway / Vpu mediated degradation of CD4 / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR2 signaling / Degradation of DVL / Peroxisomal protein import / Negative regulation of FGFR4 signaling / Stabilization of p53
Similarity search - Function
HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily ...HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / 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. / Pectin lyase fold / Pectin lyase fold/virulence factor / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / 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
Tail fiber / Ubiquitin-60S ribosomal protein L40 / DNA polymerase iota
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsBurschowsky, D. / Rudolf, F. / Rabut, G. / Herrmann, T. / Peter, M. / Wider, G.
CitationJournal: 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
DepositionApr 20, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650HELIX: DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase iota
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)13,7072
Polymers13,7072
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide DNA polymerase iota / Rad30 homolog B


Mass: 5130.650 Da / Num. of mol.: 1
Fragment: C-terminal ubiquitin-binding motif (UNP residues 487-532)
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
#2: Protein Ubiquitin


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D HN(CA)CB
1213D 1H-15N NOESY
1313D 1H-15N TOCSY
1423D 1H-13C NOESY
1523D (H)CCH-COSY
1612D 1H-15N HSQC
1722D 1H-13C HSQC
1843D HN(CA)CB
1933D 1H-15N NOESY
11033D 1H-15N TOCSY
11143D 1H-13C NOESY
11243D (H)CCH-COSY
11332D 1H-15N HSQC
11442D 1H-13C HSQC
11523D 1H-13C-filtered-13C-edited NOESY
11643D 1H-13C-filtered-13C-edited NOESY
11753D 1H-13C-filtered-13C-edited NOESY
11853D 1H-13C-AROMATIC NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2 mM [U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
21-2 mM [U-95% 13C; U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
34-8 mM DNA polymerase iota UBM1, 1-2 mM [U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
44-8 mM DNA polymerase iota UBM1, 1-2 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
51.0 mM DNA polymerase iota UBM1, 4 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMDNA polymerase iota UBM1-1[U-99% 15N]1-21
mMUbiquitin-24-81
25 mMsodium phosphate-31
25 mMsodium chloride-41
100 mMpotassium chloride-51
2 mMCHAPS-61
0.15 mMPMSF-71
0.2 %sodium azide-81
mMDNA polymerase iota UBM1-9[U-95% 13C; U-99% 15N]1-22
mMUbiquitin-104-82
25 mMsodium phosphate-112
25 mMsodium chloride-122
100 mMpotassium chloride-132
2 mMCHAPS-142
0.15 mMPMSF-152
0.2 %sodium azide-162
mMDNA polymerase iota UBM1-174-83
mMUbiquitin-18[U-99% 15N]1-23
25 mMsodium phosphate-193
25 mMsodium chloride-203
100 mMpotassium chloride-213
2 mMCHAPS-223
0.15 mMPMSF-233
0.2 %sodium azide-243
mMDNA polymerase iota UBM1-254-84
mMUbiquitin-26[U-95% 13C; U-99% 15N]1-24
25 mMsodium phosphate-274
25 mMsodium chloride-284
100 mMpotassium chloride-294
2 mMCHAPS-304
0.15 mMPMSF-314
0.2 %sodium azide-324
mMDNA polymerase iota UBM1-331-25
mMUbiquitin-34[U-95% 13C; U-99% 15N]4-85
25 mMsodium phosphate-355
25 mMsodium chloride-365
100 mMpotassium chloride-375
2 mMCHAPS-385
0.15 mMPMSF-395
0.2 %sodium azide-405
Sample conditionsIonic strength: 0.189 / pH: 6 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7502
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
MOLMOL2k.2Koradi, Billeter and Wuthrichgeometry optimization
UNIO'081.0.4T. Herrmannpeak picking
UNIO'081.0.4T. Herrmannchemical shift assignment
UNIO'081.0.4T. Herrmannstructure solution
DYANAGuntert, Braun and Wuthrichstructure solution
CARA1.8.4R. Kellerdata analysis
CARA1.8.4R. Kellerchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2862 / NOE intraresidue total count: 684 / NOE long range total count: 630 / NOE medium range total count: 723 / NOE sequential total count: 825
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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