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Solution Structure of UBM1 of murine Polymerase iota in Complex with Ubiquitin
Authors
Burschowsky, D., Rudolf, F., Rabut, G., Herrmann, T., Peter, M., Wider, G.
Assembly
UBM1-Ubiquitin complex
Entity
1. DNA polymerase iota UBM1 (polymer, Thiol state: not present), 48 monomers, 5125.608 Da Detail

GSDTSDLPLQ ALPEGVDQEV FKQLPADIQE EILSGKSREN LKGKGSLS


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

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG


Total weight
13690.34 Da
Max. entity weight
8564.731 Da
Source organism
Thomomys bottae , Homo sapiens
Exptl. method
solution NMR
Refine. method
molecular dynamics
Data set
assigned_chemical_shifts
Chem. Shift Complete
Sequence coverage: 100.0 %, Completeness: 90.5 %, Completeness (bb): 82.9 % Detail

Polymer type: polypeptide(L)

Total1H13C15N
All90.5 % (1316 of 1454)98.4 % (751 of 763)77.7 % (431 of 555)98.5 % (134 of 136)
Backbone82.9 % (598 of 721)98.8 % (239 of 242)67.3 % (243 of 361)98.3 % (116 of 118)
Sidechain98.1 % (830 of 846)98.3 % (512 of 521)97.7 % (300 of 307)100.0 % (18 of 18)
Aromatic85.7 % (36 of 42)100.0 % (21 of 21)71.4 % (15 of 21)
Methyl100.0 % (148 of 148)100.0 % (74 of 74)100.0 % (74 of 74)

1. DNA polymerase iota UBM1

GSDTSDLPLQ ALPEGVDQEV FKQLPADIQE EILSGKSREN LKGKGSLS

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 UBM1[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 %
10H2Onatural abundance5 %
Sample #2

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


#NameIsotope labelingTypeConcentration
11DNA polymerase iota UBM1[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 %
20H2Onatural abundance5 %
Sample #3

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


#NameIsotope labelingTypeConcentration
21DNA polymerase iota UBM1natural abundance1.0 ~ 2.0 mM
22Ubiquitin[U-99% 15N]4.0 ~ 8.0 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 %
30H2Onatural abundance5 %
Sample #4

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


#NameIsotope labelingTypeConcentration
31DNA polymerase iota UBM1natural abundance1.0 ~ 2.0 mM
32Ubiquitin[U-95% 13C; U-99% 15N]4.0 ~ 8.0 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 %
40H2Onatural abundance5 %
Sample #5

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


#NameIsotope labelingTypeConcentration
41DNA polymerase iota UBM1natural 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 %
50H2Onatural abundance5 %

LACS Plot; CA
Referencing offset: -0.17 ppm, Outliers: 2 Detail
LACS Plot; CB
Referencing offset: -0.17 ppm, Outliers: 2 Detail
LACS Plot; HA
Referencing offset: -0.09 ppm, Outliers: 1 Detail
Protein Blocks Logo
Calculated from 20 models in PDB: 2KWV, 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 UBM1, : 1 : 1 : 6 entities Detail
Experiments performed 17 experiments Detail
Keywords TLS, UBM, polymerase iota, ubiquitin, ubiquitin-binding motif