BMRBj - BMREntryMaster

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BMRB: 16885

2KWV

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): 83.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.5 % (1311 of 1449)	98.6 % (752 of 763)	77.8 % (432 of 555)	96.9 % (127 of 131)
Backbone	83.1 % (608 of 732)	98.0 % (248 of 253)	68.1 % (246 of 361)	96.6 % (114 of 118)
Sidechain	98.3 % (816 of 830)	98.8 % (504 of 510)	97.4 % (299 of 307)	100.0 % (13 of 13)
Aromatic	81.0 % (34 of 42)	100.0 % (21 of 21)	61.9 % (13 of 21)
Methyl	100.0 % (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

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 UBM1	[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	H2O	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 UBM1	[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	H2O	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 UBM1	natural abundance	1.0 ~ 2.0 mM
22	Ubiquitin	[U-99% 15N]	4.0 ~ 8.0 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	H2O	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 UBM1	natural abundance	1.0 ~ 2.0 mM
32	Ubiquitin	[U-95% 13C; U-99% 15N]	4.0 ~ 8.0 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	H2O	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 UBM1	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	H2O	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: -0.17 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: -0.17 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: -0.09 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 , Abstract

Related entities 1. DNA polymerase iota UBM1, : 1 : 2 : 13 entities Detail

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

Interaction partners 1. DNA polymerase iota UBM1, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 17 experiments Detail

1 3D HNCACB