BMRB Entry 51313

Title:
Assigned backbone amide and methyl chemical shifts for human Sox2 HMG domain Y72A mutant bound to DNA containing the Fgf4 motif
Deposition date:
2022-02-07
Original release date:
2023-03-20
Authors:
Malaga Gadea, Fabiana; Nikolova, Evgenia
Citation:

Citation: Malaga Gadea, Fabiana; Nikolova, Evgenia. "Structural Plasticity of Pioneer Factor Sox2 and DNA Bendability Modulate Nucleosome Engagement and Sox2-Oct4 Synergism"  J. Mol. Biol. 435, 167916-167916 (2023).
PubMed: 36495920

Assembly members:

Assembly members:
entity_1, polymer, 82 residues, Formula weight is not available
entity_2, polymer, 14 residues, Formula weight is not available
entity_3, polymer, 14 residues, Formula weight is not available

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: pET15

Entity Sequences (FASTA):

Data sets:
Data typeCount
13C chemical shifts29
15N chemical shifts68
1H chemical shifts155

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Sox2 HMG Y72A1
2DNA_strand_12
3DNA_strand_23

Entities:

Entity 1, Sox2 HMG Y72A 82 residues - Formula weight is not available

1   GLYPROASPARGVALLYSARGPROMETASN
2   ALAPHEMETVALTRPSERARGGLYGLNARG
3   ARGLYSMETALAGLNGLUASNPROLYSMET
4   HISASNSERGLUILESERLYSARGLEUGLY
5   ALAGLUTRPLYSLEULEUSERGLUTHRGLU
6   LYSARGPROPHEILEASPGLUALALYSARG
7   LEUARGALALEUHISMETLYSGLUHISPRO
8   ASPALALYSTYRARGPROARGARGLYSTHR
9   LYSTHR

Entity 2, DNA_strand_1 14 residues - Formula weight is not available

1   DGDADCDTDCDTDTDTDGDT
2   DTDTDGDG

Entity 3, DNA_strand_2 14 residues - Formula weight is not available

1   DCDCDADADADCDADADADG
2   DADGDTDC

Samples:

sample_1: Sox2 HMG Y72A, [U-13C; U-15N], 0.45 mM; DNA-Fgf4 0.5 mM; DNA-Fgf4 0.5 mM; Tris-HCl 20 mM; NaCl 25 mM; TCEP 0.5 mM; EDTA 1 mM

sample_conditions_1: ionic strength: 0.025 M; pH: 7.0; 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 HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D (H)CC(CO)NH TOCSYsample_1isotropicsample_conditions_1
3D H(CCCO)NH TOCSYsample_1isotropicsample_conditions_1

Software:

TOPSPIN - data collection

NMRPipe - data processing

NESTA-NMR - data processing

SPARKY - data analysis

NMR spectrometers:

  • Bruker Avance 600 MHz MHz

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