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124  structures 1495  species 0  interactions 32968  sequences 545  architectures

Family: HMG_box (PF00505)

Summary: HMG (high mobility group) box

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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

HMG-box Edit Wikipedia article

HMG (high mobility group) box
2LEF.png
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.
Identifiers
SymbolPF00505
PfamPF00505
InterProIPR009071
SCOPe1hsm / SUPFAM

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

Structure

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

Function

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]

References

  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 (high mobility group) box Provide feedback

No Pfam abstract.

Internal database links

External 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

Alignments

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.

  Seed
(27)
Full
(32968)
Representative proteomes UniProt
(66034)
RP15
(5958)
RP35
(14253)
RP55
(28085)
RP75
(37350)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(27)
Full
(32968)
Representative proteomes UniProt
(66034)
RP15
(5958)
RP35
(14253)
RP55
(28085)
RP75
(37350)
Alignment:
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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.

  Seed
(27)
Full
(32968)
Representative proteomes UniProt
(66034)
RP15
(5958)
RP35
(14253)
RP55
(28085)
RP75
(37350)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

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...

Trees

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.

Note: You can also download the data file for the tree.

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: Pfam-B_8 (release 1.0)
Previous IDs: HMG_box; MaoC_dehydrat_N;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 27
Number in full: 32968
Average length of the domain: 67.30 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 14.16 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.4 25.4
Trusted cut-off 25.4 25.4
Noise cut-off 25.3 25.3
Model length: 69
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Structures

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 domain has been found. There are 124 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
A0A0G2JTG6 View 3D Structure Click here
A0A0G2JTZ2 View 3D Structure Click here
A0A0G2JV60 View 3D Structure Click here
A0A0G2JVD1 View 3D Structure Click here
A0A0G2JVM8 View 3D Structure Click here
A0A0G2JWG9 View 3D Structure Click here
A0A0G2JXW5 View 3D Structure Click here
A0A0G2JY74 View 3D Structure Click here
A0A0G2K1M6 View 3D Structure Click here
A0A0G2K4F4 View 3D Structure Click here
A0A0G2K6P4 View 3D Structure Click here
A0A0G2K8D2 View 3D Structure Click here
A0A0G2KA73 View 3D Structure Click here
A0A0G2KAP8 View 3D Structure Click here
A0A0P0VHG2 View 3D Structure Click here
A0A0P0VHG2 View 3D Structure Click here
A0A0P0XPV0 View 3D Structure Click here
A0A0R0GHN1 View 3D Structure Click here
A0A0R0GIZ5 View 3D Structure Click here
A0A0R0I0W7 View 3D Structure Click here
A0A0R0KFD0 View 3D Structure Click here
A0A0R0KM01 View 3D Structure Click here
A0A0R0L7G1 View 3D Structure Click here
A0A0R0L7G1 View 3D Structure Click here
A0A0R0L9W1 View 3D Structure Click here
A0A0R4IMW9 View 3D Structure Click here
A0A0R4IQD2 View 3D Structure Click here
A0A0R4IRI6 View 3D Structure Click here
A0A0R4ITJ3 View 3D Structure Click here
A0A0R4J3U3 View 3D Structure Click here
A0A0R4J3U3 View 3D Structure Click here
A0A0R4J3U3 View 3D Structure Click here
A0A0R4J7S6 View 3D Structure Click here
A0A1D6E366 View 3D Structure Click here
A0A1D6EUL6 View 3D Structure Click here
A0A1D6EUM9 View 3D Structure Click here
A0A1D6H7X1 View 3D Structure Click here
A0A1D6HFM2 View 3D Structure Click here
A0A1D6IAX2 View 3D Structure Click here
A0A1D6KHG4 View 3D Structure Click here
A0A1D6LMN4 View 3D Structure Click here
A0A1D6LZE9 View 3D Structure Click here
A0A1D6MIE2 View 3D Structure Click here
A0A1D6NGD6 View 3D Structure Click here
A0A1D6Q6U2 View 3D Structure Click here
A0A1D8PJ67 View 3D Structure Click here
A0A1N7SZG1 View 3D Structure Click here
A0A286YBU7 View 3D Structure Click here
A0A2R8Q786 View 3D Structure Click here
A0A2R8Q9T1 View 3D Structure Click here
A0A2R8QC75 View 3D Structure Click here
A0A2R8QIG9 View 3D Structure Click here
A0A2R8QK93 View 3D Structure Click here
A0A2R8QLT0 View 3D Structure Click here
A0A2R8QTA2 View 3D Structure Click here
A0A5K7RLP0 View 3D Structure Click here
A2A472 View 3D Structure Click here
A3KNQ1 View 3D Structure Click here
A4I4D9 View 3D Structure Click here
A4I4D9 View 3D Structure Click here
B0BN99 View 3D Structure Click here
B0S640 View 3D Structure Click here
B0S7C3 View 3D Structure Click here
B0S7C3 View 3D Structure Click here
B0UXS3 View 3D Structure Click here
B2RPK0 View 3D Structure Click here
B3DJE0 View 3D Structure Click here
B6T1S6 View 3D Structure Click here
B6TNK8 View 3D Structure Click here
B6TNK8 View 3D Structure Click here
B6TNK8 View 3D Structure Click here
B7SBD2 View 3D Structure Click here
B7SZV3 View 3D Structure Click here
B8JL29 View 3D Structure Click here
C0P8W9 View 3D Structure Click here
C0PG86 View 3D Structure Click here
C6SZ57 View 3D Structure Click here
C6SZV9 View 3D Structure Click here
C9JSJ3 View 3D Structure Click here
D3Z937 View 3D Structure Click here
D3ZC69 View 3D Structure Click here
D3ZCR3 View 3D Structure Click here
D3ZGW6 View 3D Structure Click here
D3ZIU9 View 3D Structure Click here
D3ZLD0 View 3D Structure Click here
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D3ZLG3 View 3D Structure Click here
D3ZMW8 View 3D Structure Click here
D3ZMY3 View 3D Structure Click here
D3ZN59 View 3D Structure Click here
D3ZN63 View 3D Structure Click here
D3ZR96 View 3D Structure Click here
D3ZS25 View 3D Structure Click here
D3ZT52 View 3D Structure Click here
D3ZTE1 View 3D Structure Click here
D3ZZ13 View 3D Structure Click here
D3ZZD8 View 3D Structure Click here
D4A1U5 View 3D Structure Click here
D4A2N0 View 3D Structure Click here
D4A543 View 3D Structure Click here
D4A586 View 3D Structure Click here
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D4A853 View 3D Structure Click here
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E1JIT5 View 3D Structure Click here
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F1LYL9 View 3D Structure Click here
F1M106 View 3D Structure Click here
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F1M453 View 3D Structure Click here
F1M6B2 View 3D Structure Click here
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F1Q895 View 3D Structure Click here
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F1QF85 View 3D Structure Click here
F1QGP8 View 3D Structure Click here
F1QK54 View 3D Structure Click here
F1QXS5 View 3D Structure Click here
F1QZ83 View 3D Structure Click here
F1QZ83 View 3D Structure Click here
F1QZ83 View 3D Structure Click here
F1R060 View 3D Structure Click here
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F6NLJ7 View 3D Structure Click here
G3V923 View 3D Structure Click here
G5EBG6 View 3D Structure Click here
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G5EFV4 View 3D Structure Click here
I1J7R6 View 3D Structure Click here
I1JSU0 View 3D Structure Click here
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I1ND62 View 3D Structure Click here
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O00570 View 3D Structure Click here
O01683 View 3D Structure Click here
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O61348 View 3D Structure Click here
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O96028 View 3D Structure Click here
P09429 View 3D Structure Click here
P0C1G9 View 3D Structure Click here
P0CB47 View 3D Structure Click here
P0CB48 View 3D Structure Click here
P0CY16 View 3D Structure Click here
P0CY17 View 3D Structure Click here
P11632 View 3D Structure Click here
P11633 View 3D Structure Click here
P17480 View 3D Structure Click here
P17480 View 3D Structure Click here
P17480 View 3D Structure Click here
P23497 View 3D Structure Click here
P25042 View 3D Structure Click here
P25976 View 3D Structure Click here
P25976 View 3D Structure Click here
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P26583 View 3D Structure Click here
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P27347 View 3D Structure Click here
P27782 View 3D Structure Click here
P30681 View 3D Structure Click here
P33417 View 3D Structure Click here
P33417 View 3D Structure Click here
P35710 View 3D Structure Click here
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P35716 View 3D Structure Click here
P36402 View 3D Structure Click here
P36631 View 3D Structure Click here
P40630 View 3D Structure Click here
P40645 View 3D Structure Click here
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P40656 View 3D Structure Click here
P40657 View 3D Structure Click here
P41225 View 3D Structure Click here
P41848 View 3D Structure Click here
P43267 View 3D Structure Click here
P43680 View 3D Structure Click here
P47792 View 3D Structure Click here
P48431 View 3D Structure Click here
P48432 View 3D Structure Click here
P48436 View 3D Structure Click here
P52925 View 3D Structure Click here
P53783 View 3D Structure Click here
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P54277 View 3D Structure Click here
P56693 View 3D Structure Click here
P57073 View 3D Structure Click here
P59328 View 3D Structure Click here
P63158 View 3D Structure Click here
P63159 View 3D Structure Click here
P87057 View 3D Structure Click here
P93047 View 3D Structure Click here
Q00059 View 3D Structure Click here
Q00417 View 3D Structure Click here
Q02486 View 3D Structure Click here
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Q05066 View 3D Structure Click here
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Q06831 View 3D Structure Click here
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Q10666 View 3D Structure Click here
Q20201 View 3D Structure Click here
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Q23045 View 3D Structure Click here
Q24533 View 3D Structure Click here
Q24537 View 3D Structure Click here
Q2Z1R2 View 3D Structure Click here
Q32PP9 View 3D Structure Click here
Q3USZ2 View 3D Structure Click here
Q42344 View 3D Structure Click here
Q4D714 View 3D Structure Click here
Q4D714 View 3D Structure Click here
Q4DUS7 View 3D Structure Click here
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Q4V7E4 View 3D Structure Click here
Q503Z1 View 3D Structure Click here
Q54SJ6 View 3D Structure Click here
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Q55C24 View 3D Structure Click here
Q56A18 View 3D Structure Click here
Q59DN5 View 3D Structure Click here
Q59PR9 View 3D Structure Click here
Q5A220 View 3D Structure Click here
Q5PQZ5 View 3D Structure Click here
Q5QLQ9 View 3D Structure Click here
Q5TZG4 View 3D Structure Click here
Q5Z7N3 View 3D Structure Click here
Q61473 View 3D Structure Click here
Q62247 View 3D Structure Click here
Q62249 View 3D Structure Click here
Q62661 View 3D Structure Click here
Q65WY8 View 3D Structure Click here
Q66IB6 View 3D Structure Click here
Q66JW3 View 3D Structure Click here
Q69MM2 View 3D Structure Click here
Q6DGL6 View 3D Structure Click here
Q6EJB7 View 3D Structure Click here
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Q6P0E1 View 3D Structure Click here
Q6P0Z4 View 3D Structure Click here
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Q6RVD7 View 3D Structure Click here
Q6TEN5 View 3D Structure Click here
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Q76IQ7 View 3D Structure Click here
Q7M6Y2 View 3D Structure Click here
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Q7SZW4 View 3D Structure Click here
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Q800Q5 View 3D Structure Click here
Q803S1 View 3D Structure Click here
Q80W03 View 3D Structure Click here
Q80Y32 View 3D Structure Click here
Q811W0 View 3D Structure Click here
Q86BR8 View 3D Structure Click here
Q86U86 View 3D Structure Click here
Q8BSQ9 View 3D Structure Click here
Q8BU11 View 3D Structure Click here
Q8BVE8 View 3D Structure Click here
Q8CGW4 View 3D Structure Click here
Q8I5Y7 View 3D Structure Click here
Q8I616 View 3D Structure Click here
Q8IB14 View 3D Structure Click here
Q8IMA8 View 3D Structure Click here
Q8K119 View 3D Structure Click here
Q8LDF9 View 3D Structure Click here
Q8R316 View 3D Structure Click here
Q8T3B9 View 3D Structure Click here
Q8VBW5 View 3D Structure Click here
Q8WW32 View 3D Structure Click here
Q8WY36 View 3D Structure Click here
Q90XD1 View 3D Structure Click here
Q91ZW1 View 3D Structure Click here
Q924A0 View 3D Structure Click here
Q924A2 View 3D Structure Click here
Q941D1 View 3D Structure Click here
Q94234 View 3D Structure Click here
Q969G3 View 3D Structure Click here
Q96NM4 View 3D Structure Click here
Q96RK0 View 3D Structure Click here
Q99PM1 View 3D Structure Click here
Q9BL39 View 3D Structure Click here
Q9BT81 View 3D Structure Click here
Q9DC33 View 3D Structure Click here
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Q9HCS4 View 3D Structure Click here
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Q9LEF5 View 3D Structure Click here
Q9LG02 View 3D Structure Click here
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Q9MAT6 View 3D Structure Click here
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Q9T012 View 3D Structure Click here
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Q9UN79 View 3D Structure Click here
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