BMRB Entry 16936

Name: Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target methylated DNA sequence
Published: 2011-06-21

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PDB ID: 2ky8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR16936
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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:

Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target methylated DNA sequence

Deposition date:

2010-05-18

Original release date:

2011-06-21

Authors:

Williams, David; Scarsdale, Joe

Citation:

Citation: Scarsdale, J. Neel; Webb, Heather; Ginder, Gordon; Williams, David. "Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target-methylated DNA sequence." Nucleic Acids Res. 39, 6741-6752 (2011).
PubMed: 21531701

Assembly members:

Assembly members:
cMBD2, polymer, 72 residues, 7861.131 Da.
DNA-strand_1, polymer, 11 residues, 2794.885 Da.
DNA-strand_2, polymer, 11 residues, 3044.045 Da.
MN, non-polymer, 54.938 Da.

Natural source:

Natural source: Common Name: chicken Taxonomy ID: 9031 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Gallus gallus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET32a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
cMBD2: GSDKQGRTDCPALPPGWKKE EVIRKSGLSAGKSDVYYFSP SGKKFRSKPQLARYLGNAVD LSCFDFRTGKMM
DNA-strand_1: GGAATXGGCXC
DNA-strand_2: GAGCXGATXCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	307
15N chemical shifts	70
1H chemical shifts	582

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	cMBD2	1
2	DNA-strand_1	2
3	DNA-strand_2	3
4	MANGANESE (II) ION_1	4
5	MANGANESE (II) ION_2	4

Entities:

Entity 1, cMBD2 72 residues - 7861.131 Da.

1

GLY

SER

ASP

LYS

GLN

GLY

ARG

THR

ASP

CYS

2

PRO

ALA

LEU

PRO

GLY

TRP

LYS

GLU

3

GLU

VAL

ILE

ARG

LYS

SER

GLY

LEU

SER

ALA

4

GLY

LYS

SER

ASP

VAL

TYR

PHE

SER

PRO

5

SER

GLY

LYS

PHE

ARG

SER

LYS

PRO

GLN

6

LEU

ALA

ARG

TYR

LEU

GLY

ASN

ALA

VAL

ASP

7

LEU

SER

CYS

PHE

ASP

PHE

ARG

THR

GLY

LYS

8

MET

Entity 2, DNA-strand_1 11 residues - 2794.885 Da.

1

DG

DA

DT

5CM

DG

DC

THY

2

DC

Entity 3, DNA-strand_2 11 residues - 3044.045 Da.

1

DG

DA

DG

DC

5CM

DG

DA

DT

THY

DC

2

DC

Entity 4, MANGANESE (II) ION_1 - Mn - 54.938 Da.

1

MN

Samples:

sample_1: cMBD2, [U-99% 13C; U-99% 15N], 1 mM; DNA-strand_1 1 mM; DNA-strand_2 1 mM; phosphate 10 mM; sodium azide 0.02%; D20 10%; H20 90%

phage_alignment: cMBD2, [U-13C; U-15N; U-2H], 0.8 mM; DNA-strand_1 0.8 mM; DNA-strand_2 0.8 mM; pf1 bacteriophage 12 mg/mL; phosphate 10 mM; sodium azide 0.02%; D20 10%; H20 90%

PRE_sample_MN: cMBD2, [U-13C; U-15N; U-2H], 0.5 mM; DNA-strand_1 0.5 mM; DNA-strand_2 0.5 mM; MANGANESE (II) ION 0.5 mM; phosphate 10 mM; sodium azide 0.02%; D20 10%; H20 90%

PRE_sample_CA: cMBD2, [U-13C; U-15N; U-2H], 0.5 mM; DNA-strand_1 0.5 mM; DNA-strand_2 0.5 mM; CA2+ 0.5 mM; phosphate 10 mM; sodium azide 0.02%; D20 10%; H20 90%

sample_conditions_1: ionic strength: 20 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 HN(CO)CA	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 C(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D CCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
2D 13C,15N filtered NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	phage_alignment	anisotropic	sample_conditions_1
2D 1H-15N HSQC-T1	PRE_sample_MN	isotropic	sample_conditions_1
2D 1H-15N HSQC-T1	PRE_sample_CA	isotropic	sample_conditions_1
3D-HNCO-JNH	phage_alignment	anisotropic	sample_conditions_1
3D-HNCO-JNH	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC,JNCO	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC.JNCO	phage_alignment	anisotropic	sample_conditions_1
3D HNCO,JCOCA	sample_1	isotropic	sample_conditions_1
3D HNCO,JCOCA	phage_alignment	anisotropic	sample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

PIPP, Garrett - chemical shift assignment, peak picking

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

TOPSPIN, Bruker Biospin - collection

VNMR, Varian - collection

NMR spectrometers:

Varian UnityPlus 500 MHz
Bruker Avance 700 MHz

GB	NP_001012403 AAC68872 AAC68874 AAD50372 AAD50373 AAH46607
PDB	2KY8
REF	NP_001012403 NP_001108497 NP_001298000 NP_034903 XP_005074763
SP	Q9Z2E1
AlphaFold	Q9Z2E1