BMRB Entry 26771

Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR26771

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Title:
Backbone and Side-chain chemical shift assignments of C. elegans TDP2 Ubiquitin Association domain
Deposition date:
2016-03-24
Original release date:
2016-09-02
Authors:
Rao, Timsi; Aihara, Hideki
Citation:

Citation: Rao, Timsi; Gao, Rui; Takada, Saeko; Al Abo, Muthana; Chen, Xiang; Walters, Kylie; Pommier, Yves; Aihara, Hideki. "Novel TDP2-ubiquitin interactions and their importance for the repair of topoisomerase II-mediated DNA damage"  Nucleic Acids Res. 44, 10201-10215 (2016).
PubMed: 27543075

Assembly members:

Assembly members:
UBA_domain_of_Tyrosyl_DNA_phosphodiesterase_2_protein, polymer, 60 residues, 6501.1 Da.

Natural source:

Natural source:   Common Name: nematodes   Taxonomy ID: 6239   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Caenorhabditis elegans

Experimental source:

Experimental source:   Production method: chemical synthesis   Host organism: Escherichia coli   Vector: pE-SUMO

Entity Sequences (FASTA):

Entity Sequences (FASTA):
UBA_domain_of_Tyrosyl_DNA_phosphodiesterase_2_protein: SSMSDEQKLHEFAIITATDE AFAQSILQDVDWDLKKALDV FYGSEAFAEARSAAVMGASS

Data sets:
Data typeCount
13C chemical shifts232
15N chemical shifts59
1H chemical shifts317

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1C. elegans TDP2 Ubiquitin Association domain1

Entities:

Entity 1, C. elegans TDP2 Ubiquitin Association domain 60 residues - 6501.1 Da.

1   SERSERMETSERASPGLUGLNLYSLEUHIS
2   GLUPHEALAILEILETHRALATHRASPGLU
3   ALAPHEALAGLNSERILELEUGLNASPVAL
4   ASPTRPASPLEULYSLYSALALEUASPVAL
5   PHETYRGLYSERGLUALAPHEALAGLUALA
6   ARGSERALAALAVALMETGLYALASERSER

Samples:

sample_1: UBA domain of Tyrosyl DNA phosphodiesterase 2 protein, [U-99% 13C; U-99% 15N], 1.0 mM; sodium phosphate 25.0 mM; sodium chloride 50.0 mM; DSS 1.0 mM; H2O 95.0%; D2O 5.0%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1

Software:

NMRPipe v8.7, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

CcpNMR, CCPN - chemical shift assignment, data analysis, peak picking

PINE, Bahrami, Markley, Assadi, and Eghbalnia - chemical shift assignment

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

  • Bruker Avance 900 MHz

Related Database Links:

NCBI CAA21707.1

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