BMRB Entry 25066

Title:
NMR structure of UBA domain of DNA-damage-inducible 1 protein (Ddi1)
Deposition date:
2014-07-02
Original release date:
2015-02-02
Authors:
Zhang, Daoning; Fushman, David
Citation:

Citation: Nowicka, Urszula; Zhang, Daoning; Walker, Olivier; Castaneda, Calos; Krutauz, Daria; Chen, Tony; Reis, Noa; Glickman, Michael; Fushman, David. "DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain"  Structure ., .-..

Assembly members:

Assembly members:
entity, polymer, 44 residues, 4745.415 Da.

Natural source:

Natural source:   Common Name: Baker's yeast   Taxonomy ID: 4932   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pGEX 4T2

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GSATFPEQTIKQLMDLGFPR DAVVKALKQTNGNAEFAASL LFQS

Data sets:
Data typeCount
1H chemical shifts296
15N chemical shifts45

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1UBA domain of DNA-damage-inducible 1 protein (Ddi1)1

Entities:

Entity 1, UBA domain of DNA-damage-inducible 1 protein (Ddi1) 44 residues - 4745.415 Da.

First three residues 'GSA' represent a non-native affinity tag. Residue 4T represents 389T in the Ddi1 sequence.

1   GLYSERALATHRPHEPROGLUGLNTHRILE
2   LYSGLNLEUMETASPLEUGLYPHEPROARG
3   ASPALAVALVALLYSALALEULYSGLNTHR
4   ASNGLYASNALAGLUPHEALAALASERLEU
5   LEUPHEGLNSER

Samples:

sample_1: UBA, [U-100% 15N], 1 mM; D2O, [U-99% 2H], 7%; H2O 93%; sodium phosphate 20 mM

sample_2: UBA, [U-100% 15N], 0.5 mM; D2O, [U-99% 2H], 7%; H2O 43%; sodium phosphate 10 mM; C12E5 5%; n-hexanol 45%

sample_conditions_1: temperature: 298.2 K; pH: 6.8; pressure: 1 atm; ionic strength: 10 mM

sample_conditions_2: temperature: 308.2 K; pH: 6.8; pressure: 1 atm; ionic strength: 10 mM

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
RDCsample_2isotropicsample_conditions_1
RDCsample_2isotropicsample_conditions_2

Software:

CARA v1.8.1, Keller and Wuthrich - peak picking, chemical shift assignment

TOPSPIN v2.1, Bruker Biospin - collection, processing, data analysis

ARIA v2.1, Linge, O'Donoghue and Nilges - chemical shift calculation, structure solution, refinement

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

GB EDN63120.1 AAB64670 AAB82066 AAC18522 AAT92964 AHY75700
PDB
DBJ GAA22973
EMBL CAY79329
REF NP_011070
SP P40087
TPG DAA07804
AlphaFold P40087

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks