BMRB Entry 34745

Name: The Solution Structure of the Triple Mutant Methyl-CpG-Binding Domain from MeCP2 that Binds to Asymmetrically Modified DNA
Published: 2023-02-17

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PDB ID: 8alq
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34745
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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:

The Solution Structure of the Triple Mutant Methyl-CpG-Binding Domain from MeCP2 that Binds to Asymmetrically Modified DNA

Deposition date:

2022-08-01

Original release date:

2023-02-17

Authors:

Singh, H.

Citation:

Citation: Singh, H.. "Epigenetic Marks Probed by a DNA Duplex Reader via a Well-Tempered Conformational Plasticity" .

Assembly members:

Assembly members:
entity_1, polymer, 104 residues, 11905.288 Da.

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SLEDRGPMYDDPTLPEGWTR KLTQRKSGRSAGKYDAYLIN PQGKAFRNKVELIAYFEKVG DTSLDPNDFDFTVTGRGSPS RREQKPPKKPKSPKATSHHH HHHH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	220
15N chemical shifts	70
1H chemical shifts	318

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 104 residues - 11905.288 Da.

1

SER

LEU

GLU

ASP

ARG

GLY

PRO

MET

TYR

ASP

2

ASP

PRO

THR

LEU

PRO

GLU

GLY

TRP

THR

ARG

3

LYS

LEU

THR

GLN

ARG

LYS

SER

GLY

ARG

SER

4

ALA

GLY

LYS

TYR

ASP

ALA

TYR

LEU

ILE

ASN

5

PRO

GLN

GLY

LYS

ALA

PHE

ARG

ASN

LYS

VAL

6

GLU

LEU

ILE

ALA

TYR

PHE

GLU

LYS

VAL

GLY

7

ASP

THR

SER

LEU

ASP

PRO

ASN

ASP

PHE

ASP

8

PHE

THR

VAL

THR

GLY

ARG

GLY

SER

PRO

SER

9

ARG

GLU

GLN

LYS

PRO

LYS

PRO

10

LYS

SER

PRO

LYS

ALA

THR

SER

HIS

11

HIS

Samples:

sample_1: Methyl-CpG-binding domain (MBD) of MeCP2, [U-100% 13C; U-100% 15N], 0.6 mM

sample_2: Methyl-CpG-binding domain (MBD) of MeCP2, [U-100% 15N], 0.6 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6 pH*; pressure: 1 atm; temperature: 305 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 CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

CARA, Keller and Wuthrich - chemical shift assignment

Sparky, Goddard - peak picking

NMR spectrometers:

Bruker AVANCE 800 MHz

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