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41  structures 963  species 0  interactions 4302  sequences 144  architectures

Family: HMG_box_2 (PF09011)

Summary: HMG-box domain

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This is the Wikipedia entry entitled "HMG-box". More...

HMG-box Edit Wikipedia article

HMG (high mobility group) box
NMR structure of the HMG-box domain of the LEF1 protein (rainbow colored, N-terminus = blue, C-terminus = red) complexed with DNA (brown) based on the PDB: 2LEF​ coordinates.

In molecular biology, the HMG-box (high mobility group box) is a protein domain which is involved in DNA binding.[1]


The structure of the HMG-box domain contains three alpha helices separated by loops (see figure to the right).[2]


HMG-box containing proteins only bind non-B-type DNA conformations (kinked or unwound) with high affinity.[1] HMG-box domains are found in high mobility group proteins, which are involved in the regulation of DNA-dependent processes such as transcription, replication, and DNA repair, all of which require changing the conformation of chromatin.[2] The single and the double box HMG proteins alter DNA architecture by inducing bends upon binding.[3][4]


  1. ^ a b Stros M, Launholt D, Grasser KD (October 2007). "The HMG-box: a versatile protein domain occurring in a wide variety of DNA-binding proteins". Cell. Mol. Life Sci. 64 (19–20): 2590–606. doi:10.1007/s00018-007-7162-3. PMID 17599239.
  2. ^ a b Thomas JO (August 2001). "HMG1 and 2: architectural DNA-binding proteins". Biochem. Soc. Trans. 29 (Pt 4): 395–401. doi:10.1042/BST0290395. PMID 11497996.
  3. ^ D. Murugesapillai et al, DNA bridging and looping by HMO1 provides a mechanism for stabilizing nucleosome-free chromatin, Nucleic Acids Res (2014) 42 (14): 8996-9004
  4. ^ D. Murugesapillai et al, Single-molecule studies of high-mobility group B architectural DNA bending proteins, Biophys Rev (2016) doi:10.1007/s12551-016-0236-4

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

HMG-box domain Provide feedback

This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail [1].

Literature references

  1. Stros M, Launholt D, Grasser KD;, Cell Mol Life Sci. 2007;64:2590-2606.: The HMG-box: a versatile protein domain occurring in a wide variety of DNA-binding proteins. PUBMED:17599239 EPMC:17599239

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR009071

High mobility group (HMG) box domains are involved in binding DNA, and may be involved in protein-protein interactions as well. The structure of the HMG-box domain consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin. Many of these proteins are regulators of gene expression. HMG-box proteins are found in a variety of eukaryotic organisms, and can be broadly divided into two groups, based on sequence-dependent and sequence-independent DNA recognition; the former usually contain one HMG-box motif, while the latter can contain multiple HMG-box motifs.

HMG-box domains can be found in single or multiple copies in the following protein classes: HMG1 and HMG2 non-histone components of chromatin; SRY (sex determining region Y protein) involved in differential gonadogenesis; the SOX family of transcription factors [ PUBMED:12920151 ]; sequence-specific LEF1 (lymphoid enhancer binding factor 1) and TCF-1 (T-cell factor 1) involved in regulation of organogenesis and thymocyte differentiation [ PUBMED:10890911 ]; structure-specific recognition protein SSRP involved in transcription and replication; MTF1 mitochondrial transcription factor; nucleolar transcription factors UBF 1/2 (upstream binding factor) involved in transcription by RNA polymerase I; Abf2 yeast ARS-binding factor [ PUBMED:11779632 ]; yeast transcription factors lxr1, Rox1, Nhp6b and Spp41; mating type proteins (MAT) involved in the sexual reproduction of fungi [ PUBMED:12781674 ]; and the YABBY plant-specific transcription factors.

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 HMG-box (CL0114), which has the following description:

This clan includes the DNA-binding HMG-box proteins as well as the YABBY-like transcription factors.

The clan contains the following 8 members:

Ccdc124 CHDNT HMG_box HMG_box_2 HMG_box_5 MATalpha_HMGbox Protamine_like YABBY


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Curation and family details

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Seed source: pdb_2cto
Previous IDs: DUF1898;
Type: Domain
Sequence Ontology: SO:0000417
Author: Mistry J , Sammut SJ , Coggill P
Number in seed: 9
Number in full: 4302
Average length of the domain: 70.00 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 16.27 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.4 22.4
Trusted cut-off 22.4 22.4
Noise cut-off 22.3 22.3
Model length: 73
Family (HMM) version: 12
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Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence


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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 HMG_box_2 domain has been found. There are 41 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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