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BMRB: 19391

2MB7

Solution structure of MBD3 methylcytosine binding domain while bound to hydroxymethylated DNA

Authors

Williams, D.C., Scarsdale, J.N.

Assembly

MBD3

Entity

1. MBD3 (polymer, Thiol state: all free), 72 monomers, 8327.397 Da Detail

GSMERKRWEC PALPQGWERE EVPRRSGLSA GHRDVFYYSP SGKKFRSKPQ LARYLGGSMD LSTFDFRTGK ML

2. hDNA A (polymer, Thiol state: not present), 17 monomers, 5387.408 Da Detail

GAGGCGCTXG GCGGCAG

3. hDNA B (polymer, Thiol state: not present), 17 monomers, 5218.298 Da Detail

CTGCCGCXGA GCGCCTC

Total weight

18933.104 Da

Max. entity weight

8327.397 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 67.0 %, Completeness: 64.7 %, Completeness (bb): 62.2 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	64.7 % (762 of 1178)	49.3 % (382 of 775)	94.0 % (312 of 332)	95.8 % (68 of 71)
Backbone	62.2 % (402 of 646)	36.7 % (136 of 371)	97.1 % (202 of 208)	95.5 % (64 of 67)
Sidechain	71.0 % (423 of 596)	60.9 % (246 of 404)	92.0 % (173 of 188)	100.0 % (4 of 4)
Aromatic	50.0 % (78 of 156)	37.3 % (41 of 110)	79.5 % (35 of 44)	100.0 % (2 of 2)
Methyl	86.7 % (39 of 45)	79.2 % (19 of 24)	95.2 % (20 of 21)

1. MBD3

GSMERKRWEC PALPQGWERE EVPRRSGLSA GHRDVFYYSP SGKKFRSKPQ LARYLGGSMD LSTFDFRTGK ML

2. hDNA A

GAGGCGCTXG GCGGCAG

3. hDNA B

CTGCCGCXGA GCGCCTC

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MBD3	[U-99% 13C; U-99% 15N]	0.5 ~ 1.0 mM
2	hDNA_A	natural abundance	0.6 ~ 1.1 mM
3	hDNA_B	natural abundance	0.6 ~ 1.1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.17 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.17 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.09 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MB7, Strand ID: A Detail

Release date

2013-12-08

Citation

Probing the dynamic distribution of bound states for methylcytosine-binding domains on DNA
Cramer, J.M., Scarsdale, J., Walavalkar, N.M., Buchwald, W.A., Ginder, G.D., Williams, D.C.
J. Biol. Chem. (2014), 289, 1294-1302, PubMed 24307175 , DOI 10.1074/jbc.M113.512236 , Abstract

Related entities 1. MBD3, : 1 : 4 : 4 : 82 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC