- PDB-2kwv: Solution Structure of UBM1 of murine Polymerase iota in Complex w... -
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Basic information
Entry
Database: PDB / ID: 2kwv
Title
Solution Structure of UBM1 of murine Polymerase iota in Complex with Ubiquitin
Components
DNA polymerase iotaPOLI
Ubiquitin
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 / L13a-mediated translational silencing of Ceruloplasmin expression / cellular response to UV-C / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translesion synthesis / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / cytosolic ribosome / 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 / 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 / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / 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 / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / 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 / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / neuron projection morphogenesis / 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 / Asymmetric localization of PCP proteins / positive regulation of protein ubiquitination / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / Evasion by RSV of host interferon responses / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA Similarity search - Function
DNA polymerase type-Y, HhH motif / IMS family HHH motif / 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. / Ribosomal L40e family / Ribosomal_L40e ...DNA polymerase type-Y, HhH motif / IMS family HHH motif / 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. / 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
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
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
2
3D HN(CA)CB
1
2
1
3D 1H-15N NOESY
1
3
1
3D 1H-15N TOCSY
1
4
2
3D 1H-13C NOESY
1
5
2
3D (H)CCH-COSY
1
6
1
2D 1H-15N HSQC
1
7
2
2D 1H-13C HSQC
1
8
4
3D HN(CA)CB
1
9
3
3D 1H-15N NOESY
1
10
3
3D 1H-15N TOCSY
1
11
4
3D 1H-13C NOESY
1
12
4
3D (H)CCH-COSY
1
13
3
2D 1H-15N HSQC
1
14
4
2D 1H-13C HSQC
1
15
2
3D 1H-13C-filtered-13C-edited NOESY
1
16
4
3D 1H-13C-filtered-13C-edited NOESY
1
17
5
3D 1H-13C-filtered-13C-edited NOESY
1
18
5
3D 1H-13C-AROMATIC NOESY
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1-2 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% D2O
95% H2O/5% D2O
2
1-2 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% D2O
95% H2O/5% D2O
3
4-8 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% D2O
95% H2O/5% D2O
4
4-8 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% D2O
95% H2O/5% D2O
5
1.0 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% D2O
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... andKollm
refinement
TopSpin
2.1
BrukerBiospin
collection
TopSpin
2.1
BrukerBiospin
processing
MOLMOL
2k.2
Koradi, BilleterandWuthrich
geometryoptimization
UNIO'08
1.0.4
T. Herrmann
peakpicking
UNIO'08
1.0.4
T. Herrmann
chemicalshiftassignment
UNIO'08
1.0.4
T. Herrmann
structuresolution
DYANA
Guntert, BraunandWuthrich
structuresolution
CARA
1.8.4
R. Keller
dataanalysis
CARA
1.8.4
R. Keller
chemicalshiftassignment
Refinement
Method: molecular dynamics / Software ordinal: 1
NMR constraints
NOE 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 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
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