Search

NMR solution structure of the Ubiquitin like domain (UBL) of DNA-damage-inducible 1 protein (Ddi1)
Authors
Nowicka, U., Fushman, D., Chen, T.
Assembly
Ddi1UBL
Entity
1. Ddi1UBL (polymer, Thiol state: all free), 79 monomers, 8819.866 Da Detail

DLTISNELTG EIYGPIEVSE DMALTDLIAL LQADCGFDKT KHDLYYNMDI LDSNRTQSLK ELGLKTDDLL LIRGKISNS


Formula weight
8819.866 Da
Source organism
Saccharomyces cerevisiae
Exptl. method
solution NMR
Refine. method
simulated annealing
Data set
assigned_chemical_shifts
Chem. Shift Complete
Sequence coverage: 100.0 %, Completeness: 97.8 %, Completeness (bb): 99.8 % Detail

Polymer type: polypeptide(L)

Total1H13C15N
All97.8 % (884 of 904)99.6 % (464 of 466)94.9 % (336 of 354)100.0 % (84 of 84)
Backbone99.8 % (471 of 472)100.0 % (162 of 162)99.6 % (231 of 232)100.0 % (78 of 78)
Sidechain96.0 % (486 of 506)99.3 % (302 of 304)90.8 % (178 of 196)100.0 % (6 of 6)
Aromatic63.2 % (24 of 38)100.0 % (19 of 19)26.3 % (5 of 19)
Methyl99.1 % (105 of 106)100.0 % (53 of 53)98.1 % (52 of 53)

1. Ddi1UBL

DLTISNELTG EIYGPIEVSE DMALTDLIAL LQADCGFDKT KHDLYYNMDI LDSNRTQSLK ELGLKTDDLL LIRGKISNS

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 295.5 K, pH 6.8, Details 1mM Ddi1UBL sample in pH6.8 20mM Sodium Phosphate Buffer, with 3mM TCEP, containing 5% D2O.


#NameIsotope labelingTypeConcentration
1Ddi1UBL[U-100% 15N]1 mM
2D2O[U-99% 2H]5 %
3H2Onatural abundance95 %
4sodium phosphatenatural abundance20 mM
5TCEPnatural abundance3 mM
Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 295.5 K, pH 6.8, Details 1mM Ddi1UBL sample in pH6.8 20mM Sodium Phosphate Buffer, with 3mM TCEP, containing 5% D2O.


#NameIsotope labelingTypeConcentration
6Ddi1UBL[U-100% 13C; U-100% 15N]1 mM
7D2O[U-99% 2H]5 %
8H2Onatural abundance95 %
9sodium phosphatenatural abundance20 mM
10TCEPnatural abundance3 mM
Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 295.5 K, pH 6.8, Details 1mM Ddi1UBL sample in liquid crystalline medium


#NameIsotope labelingTypeConcentration
11Ddi1UBL[U-100% 15N]1 mM
12D2O[U-99% 2H]5 %
13H2Onatural abundance45 %
14sodium phosphatenatural abundance10 mM
15TCEPnatural abundance3 mM
16C12E5natural abundance5 %
17n-hexanolnatural abundance45 %

LACS Plot; CA
Referencing offset: 2.15 ppm, Outliers: 1 Detail
LACS Plot; CB
Referencing offset: 2.15 ppm, Outliers: 1 Detail
LACS Plot; HA
Referencing offset: 0.07 ppm, Outliers: 1 Detail
LACS Plot; CO
Referencing offset: 2.43 ppm, Outliers: 1 Detail
Protein Blocks Logo
Calculated from 8 models in PDB: 2MWS, Strand ID: B Detail


Release date
2015-03-22
Citation
DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin
Nowicka, U., Zhang, D., Walker, O., Castaneda, C.A., Krutauz, D., Chen, T., Reis, N., Glickman, M.H., Fushman, D.
Structure (2015), 23, 542-557, PubMed 25703377 , DOI 10.1016/j.str.2015.01.010 ,
Related entities 1. Ddi1UBL, : 1 : 4 : 6 entities Detail
Interaction partners 1. Ddi1UBL, : 10 interactors Detail
Experiments performed 14 experiments Detail
nullKeywords DNA-damage-inducible 1 protein, Ddi1, Ubiquitin like domain, UBL, NMR