BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 19939

Title: Solution structure of MBD4 methyl-cytosine binding domain bound to methylated DNA   PubMed: 25183517

Authors: Williams, David; Walavalkar, Ninad

Citation: Walavalkar, Ninad; Cramer, Jason; Buchwald, William; Scarsdale, Neel; Williams, David. "Solution structure and intramolecular exchange of methyl-cytosine binding domain protein 4 (MBD4) on DNA suggests a mechanism to scan for mCpG/TpG mismatches"  Nucleic Acids Res. ., .-. (2014).

Assembly members:
MBD4mbd, polymer, 71 residues, 8088.318 Da.
DNAfor, polymer, 10 residues, Formula weight is not available
DNArev, polymer, 10 residues, Formula weight is not available

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

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

Entity Sequences (FASTA):
MBD4mbd: GSTECRKSVPCGWERVVKQR LFGKTAGRFDVYFISPQGLK FRSKSSLANYLHKNGETSLK PEDFDFTVLSK
DNAfor: GGATXGGCTC
DNArev: GAGCXGATCC

Data sets:
Data typeCount
13C chemical shifts291
1H chemical shifts526
15N chemical shifts75

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1MBD4mbd1
2methylated DNA, 12
3methylated DNA, 23

Entities:

Entity 1, MBD4mbd 71 residues - 8088.318 Da.

1   GLYSERTHRGLUCYSARGLYSSERVALPRO
2   CYSGLYTRPGLUARGVALVALLYSGLNARG
3   LEUPHEGLYLYSTHRALAGLYARGPHEASP
4   VALTYRPHEILESERPROGLNGLYLEULYS
5   PHEARGSERLYSSERSERLEUALAASNTYR
6   LEUHISLYSASNGLYGLUTHRSERLEULYS
7   PROGLUASPPHEASPPHETHRVALLEUSER
8   LYS

Entity 2, methylated DNA, 1 10 residues - Formula weight is not available

1   DGDGDADT5CMDGDGDCDTDC

Entity 3, methylated DNA, 2 10 residues - Formula weight is not available

1   DGDADGDC5CMDGDADTDCDC

Samples:

sample_1: MBD4mbd, [U-99% 13C; U-99% 15N], 0.2 – 1.0 mM; DNAfor0.2 – 1.0 mM; DNArev0.2 – 1.0 mM; Na2PO4 10 mM

sample_2: MBD4mbd, [U-13C; U-15N; U-2H], 0.2 – 1.0 mM; DNAfor0.2 – 1.0 mM; DNArev0.2 – 1.0 mM; Pf1 phage 12 mg/mL; Na2PO4 10 mM

sample_conditions_1: temperature: 298 K; pH: 6.5; pressure: 1 atm; ionic strength: 30 mM

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D HNCOsample_2anisotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1

Software:

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

CcpNmr v2.3, CCPN - data analysis, peak picking

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

  • Bruker Avance 700 MHz

Related Database Links:

PDB
DBJ BAE02211 BAG64144 BAK62846
EMBL CAG29301 CAH89518
GB AAC68879 AAD22195 AAD50374 AAH11752 AAM00008
REF NP_001127160 NP_001263199 NP_001263200 NP_001263201 NP_001267403
SP O95243