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BMRB: 17238

2L4E

NMR structure of the UBA domain of S. cerevisiae Dcn1

Authors

Burschowsky, D., Rudolf, F., Mattle, D., Peter, M., Wider, G.

Assembly

UBA

Entity

1. UBA (polymer, Thiol state: all free), 59 monomers, 6914.547 Da Detail

GSIKRKDASP EQEAIESFTS LTKCDPKVSR KYLQRNHWNI NYALNDYYDK EIGTFTDEV

Formula weight

6914.547 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.7 %, Completeness (bb): 83.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.7 % (627 of 707)	96.5 % (358 of 371)	76.1 % (207 of 272)	96.9 % (62 of 64)
Backbone	83.4 % (292 of 350)	96.6 % (114 of 118)	70.3 % (123 of 175)	96.5 % (55 of 57)
Sidechain	94.7 % (392 of 414)	96.4 % (244 of 253)	91.6 % (141 of 154)	100.0 % (7 of 7)
Aromatic	82.4 % (56 of 68)	100.0 % (34 of 34)	63.6 % (21 of 33)	100.0 % (1 of 1)
Methyl	100.0 % (50 of 50)	100.0 % (25 of 25)	100.0 % (25 of 25)

1. Dcn1-UBA

GSIKRKDASP EQEAIESFTS LTKCDPKVSR KYLQRNHWNI NYALNDYYDK EIGTFTDEV

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.15

#	Name	Isotope labeling	Type	Concentration
1	Dcn1-UBA	[U-80% 13C; U-90% 15N]		0.6 mM
2	potassium phosphate	natural abundance		15 mM
3	potassium phosphate	natural abundance		110 mM
4	DTT	natural abundance		2 mM
5	CHAPS	natural abundance		2 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.15

#	Name	Isotope labeling	Type	Concentration
9	Dcn1-UBA	[U-90% 15N]		0.55 mM
10	potassium phosphate	natural abundance		15 mM
11	potassium phosphate	natural abundance		110 mM
12	DTT	natural abundance		2 mM
13	CHAPS	natural abundance		2 mM
14	sodium azide	natural abundance		0.05 %
15	H2O	natural abundance		95 %
16	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: -0.19 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.19 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.03 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2L4E, Strand ID: A Detail

Release date

2012-07-24

Citation

Structural analysis of the ubiquitin-associated domain (UBA) of yeast Dcn1 in complex with ubiquitin (WORKING TITLE)
Burschowsky, D., Rudolf, F., Mattle, D., Peter, M., Wider, G.
Not known

Related entities 1. UBA, : 1 : 1 : 3 : 13 entities Detail

Interaction partners 1. UBA, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 7 experiments Detail

1 3D HNCA

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.15

#	Name	Isotope labeling	Type	Concentration
1	Dcn1-UBA	[U-80% 13C; U-90% 15N]		0.6 mM
2	potassium phosphate	natural abundance		15 mM
3	potassium phosphate	natural abundance		110 mM
4	DTT	natural abundance		2 mM
5	CHAPS	natural abundance		2 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %

2 3D CBCA(CO)NH

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.15

#	Name	Isotope labeling	Type	Concentration
1	Dcn1-UBA	[U-80% 13C; U-90% 15N]		0.6 mM
2	potassium phosphate	natural abundance		15 mM
3	potassium phosphate	natural abundance		110 mM
4	DTT	natural abundance		2 mM
5	CHAPS	natural abundance		2 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %

3 3D HCCH-TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.15

#	Name	Isotope labeling	Type	Concentration
1	Dcn1-UBA	[U-80% 13C; U-90% 15N]		0.6 mM
2	potassium phosphate	natural abundance		15 mM
3	potassium phosphate	natural abundance		110 mM
4	DTT	natural abundance		2 mM
5	CHAPS	natural abundance		2 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %

4 3D 1H-15N NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.15

#	Name	Isotope labeling	Type	Concentration
9	Dcn1-UBA	[U-90% 15N]		0.55 mM
10	potassium phosphate	natural abundance		15 mM
11	potassium phosphate	natural abundance		110 mM
12	DTT	natural abundance		2 mM
13	CHAPS	natural abundance		2 mM
14	sodium azide	natural abundance		0.05 %
15	H2O	natural abundance		95 %
16	D2O	natural abundance		5 %

5 3D 1H-13C NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.15

#	Name	Isotope labeling	Type	Concentration
1	Dcn1-UBA	[U-80% 13C; U-90% 15N]		0.6 mM
2	potassium phosphate	natural abundance		15 mM
3	potassium phosphate	natural abundance		110 mM
4	DTT	natural abundance		2 mM
5	CHAPS	natural abundance		2 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %

6 3D 1H-13Caro NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.15

#	Name	Isotope labeling	Type	Concentration
1	Dcn1-UBA	[U-80% 13C; U-90% 15N]		0.6 mM
2	potassium phosphate	natural abundance		15 mM
3	potassium phosphate	natural abundance		110 mM
4	DTT	natural abundance		2 mM
5	CHAPS	natural abundance		2 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %

7 2D 1H-15N HSQC

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.15

#	Name	Isotope labeling	Type	Concentration
9	Dcn1-UBA	[U-90% 15N]		0.55 mM
10	potassium phosphate	natural abundance		15 mM
11	potassium phosphate	natural abundance		110 mM
12	DTT	natural abundance		2 mM
13	CHAPS	natural abundance		2 mM
14	sodium azide	natural abundance		0.05 %
15	H2O	natural abundance		95 %
16	D2O	natural abundance		5 %

nullKeywords neddylation, UBA, ubiquitin binding