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Solution Structure of UBM2 of murine Polymerase iota in Complex with Ubiquitin
Authors
Burschowsky, D., Rudolf, F., Rabut, G., Herrmann, T., Peter, M., Wider, G.
Assembly
UBM2 in Complex with Ubiquitin
Entity
1. DNA polymerase iota UBM2 (polymer, Thiol state: not present), 50 monomers, 5698.198 Da Detail

GSPEFDSAEE KLPFPPDIDP QVFYELPEEV QKELMAEWER AGAARPSAHR


2. Ubiquitin (polymer, Thiol state: not present), 76 monomers, 8564.731 Da Detail

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG


Total weight
14262.93 Da
Max. entity weight
8564.731 Da
Source organism
Mus musculus , Homo sapiens
Exptl. method
solution NMR
Refine. method
molecular dynamics
Data set
assigned_chemical_shifts
Chem. Shift Complete
Sequence coverage: 100.0 %, Completeness: 88.5 %, Completeness (bb): 81.7 % Detail

Polymer type: polypeptide(L)

Total1H13C15N
All88.5 % (1329 of 1501)97.1 % (765 of 788)74.8 % (433 of 579)97.8 % (131 of 134)
Backbone81.7 % (595 of 728)97.9 % (237 of 242)66.2 % (245 of 370)97.4 % (113 of 116)
Sidechain95.6 % (852 of 891)96.7 % (528 of 546)93.6 % (306 of 327)100.0 % (18 of 18)
Aromatic79.1 % (68 of 86)93.0 % (40 of 43)64.3 % (27 of 42)100.0 % (1 of 1)
Methyl100.0 % (134 of 134)100.0 % (67 of 67)100.0 % (67 of 67)

1. DNA polymerase iota UBM2

GSPEFDSAEE KLPFPPDIDP QVFYELPEEV QKELMAEWER AGAARPSAHR

2. Ubiquitin

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0


#NameIsotope labelingTypeConcentration
1DNA polymerase iota UBM2[U-99% 15N]1.0 ~ 2.0 mM
2Ubiquitinnatural abundance4.0 ~ 8.0 mM
3sodium phosphatenatural abundance25 mM
4sodium chloridenatural abundance25 mM
5potassium chloridenatural abundance100 mM
6CHAPSnatural abundance2 mM
7PMSFnatural abundance0.15 mM
8sodium azidenatural abundance0.2 % w/v
9H2Onatural abundance95 %
10D2Onatural abundance5 %
Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0


#NameIsotope labelingTypeConcentration
11DNA polymerase iota UBM2[U-95% 13C; U-99% 15N]1.0 ~ 2.0 mM
12Ubiquitinnatural abundance4.0 ~ 8.0 mM
13sodium phosphatenatural abundance25 mM
14sodium chloridenatural abundance25 mM
15potassium chloridenatural abundance100 mM
16CHAPSnatural abundance2 mM
17PMSFnatural abundance0.15 mM
18sodium azidenatural abundance0.2 % w/v
19H2Onatural abundance95 %
20D2Onatural abundance5 %
Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0


#NameIsotope labelingTypeConcentration
21DNA polymerase iota UBM2natural abundance4.0 ~ 8.0 mM
22Ubiquitin[U-99% 15N]1.0 ~ 2.0 mM
23sodium phosphatenatural abundance25 mM
24sodium chloridenatural abundance25 mM
25potassium chloridenatural abundance100 mM
26CHAPSnatural abundance2 mM
27PMSFnatural abundance0.15 mM
28sodium azidenatural abundance0.2 % w/v
29H2Onatural abundance95 %
30D2Onatural abundance5 %
Sample #4

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0


#NameIsotope labelingTypeConcentration
31DNA polymerase iota UBM2natural abundance4.0 ~ 8.0 mM
32Ubiquitin[U-95% 13C; U-99% 15N]1.0 ~ 2.0 mM
33sodium phosphatenatural abundance25 mM
34sodium chloridenatural abundance25 mM
35potassium chloridenatural abundance100 mM
36CHAPSnatural abundance2 mM
37PMSFnatural abundance0.15 mM
38sodium azidenatural abundance0.2 % w/v
39H2Onatural abundance95 %
40D2Onatural abundance5 %
Sample #5

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0


#NameIsotope labelingTypeConcentration
41DNA polymerase iota UBM2natural abundance1.0 ~ 2.0 mM
42Ubiquitin[U-95% 13C; U-99% 15N]4.0 ~ 8.0 mM
43sodium phosphatenatural abundance25 mM
44sodium chloridenatural abundance25 mM
45potassium chloridenatural abundance100 mM
46CHAPSnatural abundance2 mM
47PMSFnatural abundance0.15 mM
48sodium azidenatural abundance0.2 % w/v
49H2Onatural abundance95 %
50D2Onatural abundance5 %

LACS Plot; CA
Referencing offset: -0.3 ppm, Outliers: 2 Detail
LACS Plot; CB
Referencing offset: -0.3 ppm, Outliers: 2 Detail
LACS Plot; HA
Referencing offset: -0.11 ppm, Outliers: 1 Detail
Protein Blocks Logo
Calculated from 20 models in PDB: 2KWU, Strand ID: A, B Detail


Release date
2010-10-13
Citation
Structural analysis of the conserved ubiquitin-binding motifs (UBMs) of the translesion polymerase iota in complex with ubiquitin
Burschowsky, D., Rudolf, F., Rabut, G., Herrmann, T., Matthias, P., Wider, G.
J. Biol. Chem. (2011), 286, 1364-1373, PubMed 20929865 , DOI 10.1074/jbc.M110.135038 ,
Related entities 1. DNA polymerase iota UBM2, : 1 : 2 : 5 entities Detail
Experiments performed 17 experiments Detail
Keywords polymerase iota, ubiquitin, ubiquitin-binding motif, UBM