6C1V

MBD2 in complex with double-stranded DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA.

Liu, K., Xu, C., Lei, M., Yang, A., Loppnau, P., Hughes, T.R., Min, J.

(2018) J Biol Chem 293: 7344-7354

  • DOI: https://doi.org/10.1074/jbc.RA118.001785
  • Primary Citation of Related Structures:  
    6C1A, 6C1T, 6C1U, 6C1V, 6CNP, 6CNQ

  • PubMed Abstract: 

    • Cytosine methylation is a well-characterized epigenetic mark and occurs at both CG and non-CG sites in DNA. Both methylated CG (mCG)- and mCH (H = A, C, or T)-containing DNAs, especially mCAC-containing DNAs, are recognized by methyl-CpG-binding protein 2 (MeCP2) to regulate gene expression in neuron development ...

    Cytosine methylation is a well-characterized epigenetic mark and occurs at both CG and non-CG sites in DNA. Both methylated CG (mCG)- and mCH (H = A, C, or T)-containing DNAs, especially mCAC-containing DNAs, are recognized by methyl-CpG-binding protein 2 (MeCP2) to regulate gene expression in neuron development. However, the molecular mechanism involved in the binding of methyl-CpG-binding domain (MBD) of MeCP2 to these different DNA motifs is unclear. Here, we systematically characterized the DNA-binding selectivities of the MBD domains in MeCP2 and MBD1-4 with isothermal titration calorimetry-based binding assays, mutagenesis studies, and X-ray crystallography. We found that the MBD domains of MeCP2 and MBD1-4 bind mCG-containing DNAs independently of the sequence identity outside the mCG dinucleotide. Moreover, some MBD domains bound to both methylated and unmethylated CA dinucleotide-containing DNAs, with a preference for the CAC sequence motif. We also found that the MBD domains bind to mCA or nonmethylated CA DNA by recognizing the complementary TG dinucleotide, which is consistent with an overlooked ligand of MeCP2, i.e. the matrix/scaffold attachment regions (MARs/SARs) with a consensus sequence of 5'-GGTGT-3' that was identified in early 1990s. Our results also explain why MeCP2 exhibits similar binding affinity to both mCA- and hmCA-containing dsDNAs. In summary, our results suggest that in addition to mCG sites, unmethylated CA or TG sites also serve as DNA-binding sites for MeCP2 and other MBD-containing proteins. This discovery expands the genome-wide activity of MBD-containing proteins in gene regulation.

    Organizational Affiliation: 

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7; Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada. Electronic address: jr.min@utoronto.ca.



Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methyl-CpG-binding domain protein 2A, B, E, F79Homo sapiensMutation(s): 0 
Gene Names: MBD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBB5 (Homo sapiens)
Explore Q9UBB5 
Go to UniProtKB:  Q9UBB5
PHAROS:  Q9UBB5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBB5
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
12-mer DNAC, G12synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
12-mer DNAD, H12synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX
Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth D],
CA [auth E],
DA [auth E],
EA [auth E],
AA [auth C],
BA [auth D],
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth E],
GA [auth E],
HA [auth E],
I [auth A],
IA [auth E],
J [auth A],
JA [auth F],
K [auth A],
KA [auth F],
L [auth A],
LA [auth F],
M [auth A],
MA [auth F],
N [auth A],
NA [auth G],
O [auth A],
OA [auth G],
P [auth A],
PA [auth G],
Q [auth A],
QA [auth G],
R [auth B],
RA [auth H],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth C],
Y [auth C],
Z [auth C]
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: P 1
  • Diffraction Data: https://doi.org/10.18430/M36C1V
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.013α = 84.5
b = 40.198β = 85.48
c = 105.158γ = 62.71
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-23
    Changes: Data collection, Database references