BMRB Entry 19074

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR19074

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Title:
1H, 13C, 15N chemical shift assignments of Dido PHD domain in complex with peptide H3K4me3
Deposition date:
2013-03-05
Original release date:
2013-05-30
Authors:
Santiveri, Clara; Perez-Canadillas, Jose; Jimenez, M Angeles
Citation:

Citation: Santiveri, Clara; Garcia-Mayoral, M. Flor; Perez-Canadillas, Jose; Jimenez, M. Angeles. "NMR structure note: PHD domain from death inducer obliterator protein and its interaction with H3K4me3."  J. Biomol. NMR 56, 183-190 (2013).
PubMed: 23579637

Assembly members:

Assembly members:
Dido_PHD, polymer, 61 residues, 7048.059 Da.
Dido_PHD, polymer, 61 residues, 7048.059 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET28

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Dido_PHD: GSMDPNALYCICRQPHNNRF MICCDRCEEWFHGDCVGISE ARGRLLERNGEDYICPNCTI L
Dido_PHD: GSMDPNALYCICRQPHNNRF MICCDRCEEWFHGDCVGISE ARGRLLERNGEDYICPNCTI L

Data sets:
Data typeCount
13C chemical shifts267
15N chemical shifts66
1H chemical shifts383

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22
3ZINC ION_13
4ZINC ION_23

Entities:

Entity 1, entity_1 61 residues - 7048.059 Da.

Residues 1-3, GSM, are the cloning tag. Residues 4-61 correspond to residues 265-322 from human Dido or to residues 262-319 from mouse Dido.

1   GLYSERMETASPPROASNALALEUTYRCYS
2   ILECYSARGGLNPROHISASNASNARGPHE
3   METILECYSCYSASPARGCYSGLUGLUTRP
4   PHEHISGLYASPCYSVALGLYILESERGLU
5   ALAARGGLYARGLEULEUGLUARGASNGLY
6   GLUASPTYRILECYSPROASNCYSTHRILE
7   LEU

Entity 2, entity_2 61 residues - 7048.059 Da.

Residues 1-3, GSM, are the cloning tag. Residues 4-61 correspond to residues 265-322 from human Dido or to residues 262-319 from mouse Dido.

1   GLYSERMETASPPROASNALALEUTYRCYS
2   ILECYSARGGLNPROHISASNASNARGPHE
3   METILECYSCYSASPARGCYSGLUGLUTRP
4   PHEHISGLYASPCYSVALGLYILESERGLU
5   ALAARGGLYARGLEULEUGLUARGASNGLY
6   GLUASPTYRILECYSPROASNCYSTHRILE
7   LEU

Entity 3, ZINC ION_1 - 65.409 Da.

1   ZN

Samples:

sample_1: Dido PHD, [U-99% 13C; U-99% 15N], 0.1 mM; H3K4me3 0.4 mM; potassium phosphate 10 uM; TCEP 100 uM; sodium azide 0.01%; H2O 90%; D2O 10%; DSS 10 uM

sample_conditions_1: ionic strength: 10 mM; 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
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1

Software:

No software information available

NMR spectrometers:

  • Bruker Avance 800 MHz

Related Database Links:

UNP Q9BTC0 Q8C9B9 Q9BTC0 Q8C9B9
BMRB 18963 18963
PDB
DBJ BAA20791 BAA92094 BAC31270 BAC97927 BAE88140 BAA20791 BAA92094 BAC31270 BAC97927 BAE88140
EMBL CAB48401 CAG31367 CAH89967 CAB48401 CAG31367 CAH89967
GB AAH00770 AAH04237 AAH14489 AAH29110 AAH96662 AAH00770 AAH04237 AAH14489 AAH29110 AAH96662
REF NP_001124926 NP_001180298 NP_001180299 NP_001278361 NP_001278362 NP_001124926 NP_001180298 NP_001180299 NP_001278361 NP_001278362
SP Q8C9B9 Q9BTC0 Q8C9B9 Q9BTC0
AlphaFold Q9UFB6 Q9WV00 Q9UFB6 Q9WV00 Q8C9B9 Q9BTC0 Q8C9B9 Q9BTC0

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