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BMRB: 17239

2L4F

NMR structure of the UBA domain of S. cerevisiae Dcn1 bound to ubiquitin

Authors

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

Assembly

UBA+Ub complex

Entity

1. Dcn1-UBA (polymer, Thiol state: all free), 59 monomers, 6914.547 Da Detail

GSIKRKDASP EQEAIESFTS LTKCDPKVSR KYLQRNHWNI NYALNDYYDK EIGTFTDEV

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

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

Total weight

15479.278 Da

Max. entity weight

8564.731 Da

Source organism

Saccharomyces cerevisiae , Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 45.2 %, Completeness: 40.0 %, Completeness (bb): 37.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	40.0 % (646 of 1616)	44.1 % (374 of 849)	33.4 % (208 of 622)	44.1 % (64 of 145)
Backbone	37.6 % (301 of 800)	44.3 % (121 of 273)	31.0 % (123 of 397)	43.8 % (57 of 130)
Sidechain	42.6 % (402 of 943)	43.9 % (253 of 576)	40.3 % (142 of 352)	46.7 % (7 of 15)
Aromatic	56.0 % (56 of 100)	68.0 % (34 of 50)	42.9 % (21 of 49)	100.0 % (1 of 1)
Methyl	33.8 % (50 of 148)	33.8 % (25 of 74)	33.8 % (25 of 74)

1. Dcn1-UBA

GSIKRKDASP EQEAIESFTS LTKCDPKVSR KYLQRNHWNI NYALNDYYDK EIGTFTDEV

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 6.15

#	Name	Isotope labeling	Concentration
1	Dcn1-UBA	[U-80% 13C; U-90% 15N]	0.8 mM
2	sodium chloride	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	0.02 %
7	sodium chloride	natural abundance	25 mM
8	ubiquitin	natural abundance	3.2 mM
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 6.15

#	Name	Isotope labeling	Concentration
11	Dcn1-UBA	[U-90% 15N]	0.5 mM
12	sodium phosphate	natural abundance	15 mM
13	potassium phosphate	natural abundance	110 mM
14	DTT	natural abundance	2 mM
15	CHAPS	natural abundance	2 mM
16	sodium azide	natural abundance	0.02 %
17	sodium chloride	natural abundance	25 mM
18	ubiquitin	natural abundance	2 mM
19	H2O	natural abundance	95 %
20	D2O	natural abundance	5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.101329

Referencing offset: -0.36 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.101329

Referencing offset: -0.36 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.101329

Referencing offset: 0.03 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2L4F, 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. Dcn1-UBA, : 1 : 1 : 3 : 13 entities Detail

Related entities 2. ubiquitin, : 92 : 6 : 46 : 182 entities Detail

Interaction partners 1. Dcn1-UBA, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 7 experiments Detail

1 3D HCCH-COSY