BMRB Entry 26978

Name: MeCP2 bound to methylated DNA
Published: 2017-05-23

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR26978

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

MeCP2 bound to methylated DNA

Deposition date:

2016-12-20

Original release date:

2017-05-23

Authors:

Sperlazza, M. Jeannette; David, Williams

Citation:

Citation: Sperlazza, M. Jeannette; Bilinovich, Stephanie; Sinanan, Leander; Javier, Fatima; Williams, David. "Structural Basis of MeCP2 Distribution on Non-CpG Methylated and Hydroxymethylated DNA" J. Mol. Biol. 429, 1581-1594 (2017).
PubMed: 28450074

Assembly members:

Assembly members:
MeCP2_MBD, polymer, 89 residues, Formula weight is not available
BDNF_DNA, polymer, 19 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: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
MeCP2_MBD: MASASPKQRRSIIRDRGPMY DDPTLPEGWTRKLKQRKSGR SAGKYDVYLINPQGKAFRSK VELIAYFEKVGDTSLDPNDF DFTVTGRGS
BDNF_DNA: TAGAAGAATTCXGTTCCAG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	266
15N chemical shifts	72
1H chemical shifts	305

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	MeCP2	1
2	DNA, chain 1	2
3	DNA, chain 2	2

Entities:

Entity 1, MeCP2 89 residues - Formula weight is not available

1

MET

ALA

SER

ALA

SER

PRO

LYS

GLN

ARG

2

SER

ILE

ARG

ASP

ARG

GLY

PRO

MET

TYR

3

ASP

PRO

THR

LEU

PRO

GLU

GLY

TRP

THR

4

ARG

LYS

LEU

LYS

GLN

ARG

LYS

SER

GLY

ARG

5

SER

ALA

GLY

LYS

TYR

ASP

VAL

TYR

LEU

ILE

6

ASN

PRO

GLN

GLY

LYS

ALA

PHE

ARG

SER

LYS

7

VAL

GLU

LEU

ILE

ALA

TYR

PHE

GLU

LYS

VAL

8

GLY

ASP

THR

SER

LEU

ASP

PRO

ASN

ASP

PHE

9

ASP

PHE

THR

VAL

THR

GLY

ARG

GLY

SER

Entity 2, DNA, chain 1 19 residues - Formula weight is not available

double stranded DNA X = methyl-cytosine

1

DT

DA

DG

DA

DG

DA

DT

2

DC

1MC

DG

DT

DC

DA

DG

Samples:

sample_1: MeCP2 MBD, [U-99% 13C; U-99% 15N], 0.75 mM; BDNF DNA 0.75 mM; sodium phosphate 10 mM; sodium azide 0.02 % w/v; DTT 1 mM

sample_conditions_1: ionic strength: 25 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1

Software:

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

CcpNMR, CCPN - chemical shift assignment, peak picking

NMR spectrometers:

Bruker Avance 700 MHz

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