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66  structures 647  species 0  interactions 8958  sequences 287  architectures

Family: MBD (PF01429)

Summary: Methyl-CpG binding domain

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Methyl-CpG binding domain Provide feedback

The Methyl-CpG binding domain (MBD) binds to DNA that contains one or more symmetrically methylated CpGs [1]. DNA methylation in animals is associated with alterations in chromatin structure and silencing of gene expression. MBD has negligible non-specific affinity for DNA. In vitro foot-printing with MeCP2 showed the MBD can protect a 12 nucleotide region surrounding a methyl CpG pair [1]. MBDs are found in several Methyl-CpG binding proteins and also DNA demethylase [2].

Literature references

  1. Nan X, Meehan RR, Bird A; , Nucleic Acids Res 1993;21:4886-4892.: Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. PUBMED:8177735 EPMC:8177735

  2. Bhattacharya SK, Ramchandani S, Cervoni N, Szyf M; , Nature 1999;397:579-583.: A mammalian protein with specific demethylase activity for mCpG DNA. PUBMED:10050851 EPMC:10050851

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001739

Methylation at CpG dinucleotide, the most common DNA modification in eukaryotes, has been correlated with gene silencing associated with various phenomena such as genomic imprinting, transposon and chromosome X inactivation, differentiation, and cancer. Effects of DNA methylation are mediated through proteins which bind to symmetrically methylated CpGs. Such proteins contain a specific domain of ~70 residues, the methyl-CpG-binding domain (MBD), which is linked to additional domains associated with chromatin, such as the bromodomain, the AT hook motif,the SET domain, or the PHD finger. MBD-containing proteins appear to act as structural proteins, which recruit a variety of histone deacetylase (HDAC) complexes and chromatin remodelling factors, leading to chromatin compaction and, consequently, to transcriptional repression. The MBD of MeCP2, MBD1, MBD2, MBD4 and BAZ2 mediates binding to DNA, in case of MeCP2, MBD1 and MBD2 preferentially to methylated CpG. In case of human MBD3 and SETDB1 the MBD has been shown to mediate protein-protein interactions [ PUBMED:12529184 , PUBMED:12787239 ].

The MBD folds into an alpha/beta sandwich structure comprising a layer of twisted beta sheet, backed by another layer formed by the alpha1 helix and a hairpin loop at the C terminus. These layers are both amphipathic, with the alpha1 helix and the beta sheet lying parallel and the hydrophobic faces tightly packed against each other. The beta sheet is composed of two long inner strands (beta2 and beta3) sandwiched by two shorter outer strands (beta1 and beta4) [ PUBMED:11371345 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan MBD-like (CL0081), which has the following description:

This clan contains proteins with a distinctive three stranded DNA-binding domain [1].

The clan contains the following 10 members:

AP2 Arm-DNA-bind_1 Arm-DNA-bind_2 Arm-DNA-bind_3 Arm-DNA-bind_4 Arm-DNA-bind_5 CedA Integrase_DNA MBD MBDa


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

Representative proteomes UniProt
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Representative proteomes UniProt

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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Bateman A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 14
Number in full: 8958
Average length of the domain: 77.60 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 8.41 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 77
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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The tree shows the occurrence of this domain across different species. More...


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the MBD domain has been found. There are 66 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0B4KGZ0 View 3D Structure Click here
A0A0G2K175 View 3D Structure Click here
A0A0G2K5A7 View 3D Structure Click here
A0A0N7KIM4 View 3D Structure Click here
A0A0P0W721 View 3D Structure Click here
A0A0P0W7F1 View 3D Structure Click here
A0A0P0W8A4 View 3D Structure Click here
A0A0R0HXA8 View 3D Structure Click here
A0A0R0K8M4 View 3D Structure Click here
A0A0R4INE2 View 3D Structure Click here
A0A0R4IVN8 View 3D Structure Click here
A0A1D6ESG6 View 3D Structure Click here
A0A1D6FGI9 View 3D Structure Click here
A0A1D6GLD8 View 3D Structure Click here
A0A1D6I7F9 View 3D Structure Click here
A0A1D6JE38 View 3D Structure Click here
A0A1D6KHW6 View 3D Structure Click here
A0A1D6KW59 View 3D Structure Click here
A0A1D6KWW9 View 3D Structure Click here
A0A1D6MVE6 View 3D Structure Click here
A0A1D6MVJ4 View 3D Structure Click here
A0A1D6PU69 View 3D Structure Click here
A0A2R8RLX8 View 3D Structure Click here
A2AUY4 View 3D Structure Click here
A3BF50 View 3D Structure Click here
B7EB50 View 3D Structure Click here
C6T9F2 View 3D Structure Click here
C6TGT6 View 3D Structure Click here
C6TKN4 View 3D Structure Click here
D4A986 View 3D Structure Click here
D4A9W8 View 3D Structure Click here
F1RAZ1 View 3D Structure Click here
I1JWB8 View 3D Structure Click here
I1KDC1 View 3D Structure Click here
I1KJG1 View 3D Structure Click here
I1KJW5 View 3D Structure Click here
I1KP74 View 3D Structure Click here
I1M022 View 3D Structure Click here
I1M4T4 View 3D Structure Click here
I1M5U1 View 3D Structure Click here