BMRB Entry 31134

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31134
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Title:
Solution NMR structure of human DNMT1 N-terminal alpha-helical domain
Deposition date:
2023-12-09
Original release date:
2024-02-26
Authors:
Hu, Q.; Botuyan, M.; Mer, G.
Citation:

Citation: Hu, Q.; Botuyan, M.; Mer, G.. "Identification of a conserved alpha-helical domain at the N-terminus of human DNA methyl transferase 1"  J. Biol. Chem. 300, 105775-105775 (2024).
PubMed: 38382673

Assembly members:

Assembly members:
entity_1, polymer, 81 residues, 9494.941 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: pTEV

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GHMPAISLPDDVRRRLKDLE RDSLTEKECVKEKLNLLHEF LQTEIKNQLCDLETKLRKEE LSEEGYLAKVKSLLNKDLSL E

Data sets:
Data typeCount
13C chemical shifts353
15N chemical shifts80
1H chemical shifts593

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 81 residues - 9494.941 Da.

1   GLYHISMETPROALAILESERLEUPROASP
2   ASPVALARGARGARGLEULYSASPLEUGLU
3   ARGASPSERLEUTHRGLULYSGLUCYSVAL
4   LYSGLULYSLEUASNLEULEUHISGLUPHE
5   LEUGLNTHRGLUILELYSASNGLNLEUCYS
6   ASPLEUGLUTHRLYSLEUARGLYSGLUGLU
7   LEUSERGLUGLUGLYTYRLEUALALYSVAL
8   LYSSERLEULEUASNLYSASPLEUSERLEU
9   GLU

Samples:

sample_1: DNMT1, [U-13C; U-15N], 1 mM; MES/Bis-Tris 20 mM; sodium chloride 50 mM

sample_2: DNMT1, [U-15N], 1 mM; MES/Bis-Tris 20 mM; sodium chloride 50 mM

sample_3: DNMT1, [U-13C; U-15N], 1 mM; MES/Bis-Tris 20 mM; sodium chloride 50 mM

sample_4: DNMT1, [U-15N], 1 mM; MES/Bis-Tris 20 mM; sodium chloride 50 mM; pentaethylene glycol monododecyl ether (C12E5) 5%; n-hexanol 95%

sample_conditions_1: ionic strength: 50 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_3isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-15N IPAP HSQCsample_4anisotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

Sparky, Goddard - chemical shift assignment, peak picking, processing

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TALOS+, Shen, Delaglio, Cornilescu and Bax - geometry optimization

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

  • Bruker AVANCE III 700 MHz

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