BMRBj - BMREntryMaster

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BMRB: 16880

2KWU

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: 89.6 %, Completeness (bb): 84.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.6 % (1339 of 1494)	96.6 % (761 of 788)	78.4 % (454 of 579)	97.6 % (124 of 127)
Backbone	84.2 % (620 of 736)	97.2 % (243 of 250)	71.4 % (264 of 370)	97.4 % (113 of 116)
Sidechain	95.5 % (837 of 876)	96.3 % (518 of 538)	94.2 % (308 of 327)	100.0 % (11 of 11)
Aromatic	81.4 % (70 of 86)	93.0 % (40 of 43)	69.0 % (29 of 42)	100.0 % (1 of 1)
Methyl	100.0 % (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

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Concentration
1	DNA polymerase iota UBM2	[U-99% 15N]	1.0 ~ 2.0 mM
2	Ubiquitin	natural abundance	4.0 ~ 8.0 mM
3	sodium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM
5	potassium chloride	natural abundance	100 mM
6	CHAPS	natural abundance	2 mM
7	PMSF	natural abundance	0.15 mM
8	sodium azide	natural abundance	0.2 % w/v
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

Sample #2

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

#	Name	Isotope labeling	Concentration
11	DNA polymerase iota UBM2	[U-95% 13C; U-99% 15N]	1.0 ~ 2.0 mM
12	Ubiquitin	natural abundance	4.0 ~ 8.0 mM
13	sodium phosphate	natural abundance	25 mM
14	sodium chloride	natural abundance	25 mM
15	potassium chloride	natural abundance	100 mM
16	CHAPS	natural abundance	2 mM
17	PMSF	natural abundance	0.15 mM
18	sodium azide	natural abundance	0.2 % w/v
19	H2O	natural abundance	95 %
20	D2O	natural abundance	5 %

Sample #3

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

#	Name	Isotope labeling	Concentration
21	DNA polymerase iota UBM2	natural abundance	4.0 ~ 8.0 mM
22	Ubiquitin	[U-99% 15N]	1.0 ~ 2.0 mM
23	sodium phosphate	natural abundance	25 mM
24	sodium chloride	natural abundance	25 mM
25	potassium chloride	natural abundance	100 mM
26	CHAPS	natural abundance	2 mM
27	PMSF	natural abundance	0.15 mM
28	sodium azide	natural abundance	0.2 % w/v
29	H2O	natural abundance	95 %
30	D2O	natural abundance	5 %

Sample #4

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

#	Name	Isotope labeling	Concentration
31	DNA polymerase iota UBM2	natural abundance	4.0 ~ 8.0 mM
32	Ubiquitin	[U-95% 13C; U-99% 15N]	1.0 ~ 2.0 mM
33	sodium phosphate	natural abundance	25 mM
34	sodium chloride	natural abundance	25 mM
35	potassium chloride	natural abundance	100 mM
36	CHAPS	natural abundance	2 mM
37	PMSF	natural abundance	0.15 mM
38	sodium azide	natural abundance	0.2 % w/v
39	H2O	natural abundance	95 %
40	D2O	natural abundance	5 %

Sample #5

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

#	Name	Isotope labeling	Concentration
41	DNA polymerase iota UBM2	natural abundance	1.0 ~ 2.0 mM
42	Ubiquitin	[U-95% 13C; U-99% 15N]	4.0 ~ 8.0 mM
43	sodium phosphate	natural abundance	25 mM
44	sodium chloride	natural abundance	25 mM
45	potassium chloride	natural abundance	100 mM
46	CHAPS	natural abundance	2 mM
47	PMSF	natural abundance	0.15 mM
48	sodium azide	natural abundance	0.2 % w/v
49	H2O	natural abundance	95 %
50	D2O	natural abundance	5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.3 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.3 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

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 , Abstract

Related entities 1. DNA polymerase iota UBM2, : 1 : 3 : 13 entities Detail

Related entities 2. Ubiquitin, : 92 : 6 : 47 : 182 entities Detail

Experiments performed 17 experiments Detail

1 3D HNCACB