BMRB Entry 52660

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52660

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Title:
Backbone chemical shifts of the human MBD2 DNA-binding domain
Deposition date:
2024-10-25
Original release date:
2026-02-03
Authors:
Le Meur, Remy; Erdmann, Diane; Nguyen, Minh-Ha; Arimondo, Paola; Guijarro, J. Inaki
Citation:

Citation: Contreras, Jean; Vichier-Guerre, Sophie; Dugue, Laurence; Bonhomme, Frederic; Jallet, Corinne; Nguyen, Minh-Ha; Vitorge, Bruno; Feoli, Alessandra; Sbardella, Gianluca; Guijarro, J. Inaki; Arimondo, Paola. "In Quest of Chemical Probes for DNA Methylation Reader Proteins: Nucleoside and Dimer Analogues of 5-Methylcytosine Interact with MBD2"  Angew. Chem. Int. Ed. Engl. 64, e202425599-e202425599 (2025).
PubMed: 40272948

Assembly members:

Assembly members:
entity_1, polymer, 79 residues, 8741.21 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: pGEX-6p-2-GST-MBD2

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPLGSGKRMDCPALPPGWKK EEVIRKSGLSAGKSDVYYFS PSGKKFRSKPQLARYLGNTV DLSSFDFRTGKMMPSKLQK

Data sets:
Data typeCount
13C chemical shifts159
15N chemical shifts103
1H chemical shifts103

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1MBD21

Entities:

Entity 1, MBD2 79 residues - 8741.21 Da.

The first 4 residues of the construct do not belong to the original sequence.

1   GLYPROLEUGLYSERGLYLYSARGMETASP
2   CYSPROALALEUPROPROGLYTRPLYSLYS
3   GLUGLUVALILEARGLYSSERGLYLEUSER
4   ALAGLYLYSSERASPVALTYRTYRPHESER
5   PROSERGLYLYSLYSPHEARGSERLYSPRO
6   GLNLEUALAARGTYRLEUGLYASNTHRVAL
7   ASPLEUSERSERPHEASPPHEARGTHRGLY
8   LYSMETMETPROSERLYSLEUGLNLYS

Samples:

sample_1: methyl-CpG-binding domain protein 2, [U-98% 13C; U-98% 15N], 500 uM; sodium phosphate 10 mM; NaCl 120 mM; TCEP 1 mM

sample_2: methyl-CpG-binding domain protein 2, [U-98% 15N], 35 uM; HEPES 50 mM; NaCl 120 mM; TCEP 1 mM

sample_conditions_1: ionic strength: 130 mM; pH: 6.5; pressure: 1 atm; temperature: 293.15 K

sample_conditions_2: ionic strength: 170 mM; pH: 7; pressure: 1 atm; temperature: 291.15 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D Best-HNCOsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D Best-HNCAsample_1isotropicsample_conditions_1
3D Best-HN(CA)COsample_1isotropicsample_conditions_1
3D Best-HNCACBsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_2

Software:

TOPSPIN v3.6.3 - collection, processing

CcpNMR v2.5.2 - chemical shift assignment, data analysis

NMR spectrometers:

  • Bruker AVANCE III HD 600 MHz

Related Database Links:

GB KAI2586930.1

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