BMRB Entry 19939

Name: Solution structure of MBD4 methyl-cytosine binding domain bound to methylated DNA
Published: 2014-09-05

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PDB ID: 2moe
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19939
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of MBD4 methyl-cytosine binding domain bound to methylated DNA

Deposition date:

2014-04-24

Original release date:

2014-09-05

Authors:

Williams, David; Walavalkar, Ninad

Citation:

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).
PubMed: 25183517

Assembly members:

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:

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: pET32

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	291
1H chemical shifts	526
15N chemical shifts	75

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	MBD4mbd	1
2	methylated DNA, 1	2
3	methylated DNA, 2	3

Entities:

Entity 1, MBD4mbd 71 residues - 8088.318 Da.

1

GLY

SER

THR

GLU

CYS

ARG

LYS

SER

VAL

PRO

2

CYS

GLY

TRP

GLU

ARG

VAL

LYS

GLN

ARG

3

LEU

PHE

GLY

LYS

THR

ALA

GLY

ARG

PHE

ASP

4

VAL

TYR

PHE

ILE

SER

PRO

GLN

GLY

LEU

LYS

5

PHE

ARG

SER

LYS

SER

LEU

ALA

ASN

TYR

6

LEU

HIS

LYS

ASN

GLY

GLU

THR

SER

LEU

LYS

7

PRO

GLU

ASP

PHE

ASP

PHE

THR

VAL

LEU

SER

8

LYS

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

1

DG

DA

DT

5CM

DG

DC

DT

DC

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

1

DG

DA

DG

DC

5CM

DG

DA

DT

DC

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 CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_2	anisotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

PDB	2MOE 4LG7
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
AlphaFold	O95243

BMRB Entry 19939

Additional metadata:

Assembly:

Entities:

Samples:

Experiments:

Software:

NMR spectrometers:

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