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91  structures 347  species 0  interactions 4301  sequences 108  architectures

Family: RHD_DNA_bind (PF00554)

Summary: Rel homology DNA-binding domain

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This is the Wikipedia entry entitled "Rel homology domain". More...

Rel homology domain Edit Wikipedia article

Rel homology domain (RHD)
1SVC.png
Top view of the crystallographic structure of a homodimer of the NFKB1 protein (green and magenta) bound to DNA (brown).[1]
Identifiers
Symbol RHD
Pfam PF00554
InterPro IPR011539
PROSITE PDOC00924
SCOP 1svc
SUPERFAMILY 1svc
CDD cd07827

The Rel homology domain (RHD) is a protein domain found in a family of eukaryotic transcription factors, which includes NF-κB, NFAT, among others. Some of these transcription factors appear to form multi-protein DNA-bound complexes.[2] Phosphorylation of the RHD appears to play a role in the regulation of some of these transcription factors, acting to modulate the expression of their target genes.[3] The RHD is composed of two immunoglobulin-like beta barrel subdomains that grip the DNA in the major groove. The N-terminal specificity domain resembles the core domain of the p53 transcription factor, and contains a recognition loop that interacts with DNA bases. The C-terminal dimerization domain contains the site for interaction with I-kappaB.[1]

References

  1. ^ a b PDB: 1SVC​;Müller CW, Rey FA, Sodeoka M, Verdine GL, Harrison SC (January 1995). "Structure of the NF-kappa B p50 homodimer bound to DNA". Nature. 373 (6512): 311–7. doi:10.1038/373311a0. PMID 7830764. 
  2. ^ Wolberger C (October 1998). "Combinatorial transcription factors". Curr. Opin. Genet. Dev. 8 (5): 552–9. doi:10.1016/S0959-437X(98)80010-5. PMID 9794820. 
  3. ^ Anrather J, Racchumi G, Iadecola C (January 2005). "cis-acting, element-specific transcriptional activity of differentially phosphorylated nuclear factor-kappa B". J. Biol. Chem. 280 (1): 244–52. doi:10.1074/jbc.M409344200. PMID 15516339. 

This article incorporates text from the public domain Pfam and InterPro IPR011539


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.

Rel homology DNA-binding domain Provide feedback

Proteins containing the Rel homology domain (RHD) are eukaryotic transcription factors. The RHD is composed of two structural domains. This is the N-terminal DNA-binding domain that is similar to that found in P53. The C-terminal domain has an immunoglobulin-like fold (See PF16179) that functions as a dimerisation domain [1-2].

Literature references

  1. Moorthy AK, Huang DB, Wang VY, Vu D, Ghosh G;, J Mol Biol. 2007;373:723-734.: X-ray structure of a NF-kappaB p50/RelB/DNA complex reveals assembly of multiple dimers on tandem kappaB sites. PUBMED:17869269 EPMC:17869269


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011539

The Rel homology domain (RHD) is found in a family of eukaryotic transcription factors, which includes NF-kappaB, Dorsal, Relish, NFAT, among others. The RHD is composed of two structural domains: the N-terminal DNA binding domain that is similar to that found in P53, the C-terminal domain has an immunoglobulin-like fold (See ) that functions as a dimerisation domain. This entry represents the N-terminal DNA binding domain [ PUBMED:17869269 ].

Some of these transcription factors appear to form multi-protein DNA-bound complexes [ PUBMED:9794820 ]. Phosphorylation of the RHD appears to play a role in the regulation of some of these transcription factors, acting to modulate the expression of their target genes [ PUBMED:15516339 ]. The RHD is composed of two immunoglobulin-like beta-barrel subdomains that grip the DNA in the major groove. The N-terminal specificity domain resembles the core domain of the p53 transcription factor, and contains a recognition loop that interacts with DNA bases; the C-terminal dimerisation domain contains the site for interaction with I-kappaB [ PUBMED:7830764 ].

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 P53-like (CL0073), which has the following description:

This clan contains a variety of DNA-binding domains that contain an immunoglobulin-like fold. It includes the DNA-binding domains of NF-kappaB, NFAT, p53, STAT-1, the T-domain and the Runt domain [1].

The clan contains the following 9 members:

CEP1-DNA_bind LAG1-DNAbind NDT80_PhoG P53 PAD_M RHD_DNA_bind Runt STAT_bind T-box

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...

View options

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
(21)
Full
(4301)
Representative proteomes UniProt
(7952)
RP15
(432)
RP35
(1331)
RP55
(3537)
RP75
(4969)
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PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(21)
Full
(4301)
Representative proteomes UniProt
(7952)
RP15
(432)
RP35
(1331)
RP55
(3537)
RP75
(4969)
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
(21)
Full
(4301)
Representative proteomes UniProt
(7952)
RP15
(432)
RP35
(1331)
RP55
(3537)
RP75
(4969)
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: SCOP
Previous IDs: RHD;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Eberhardt R
Number in seed: 21
Number in full: 4301
Average length of the domain: 160.40 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 19.34 %

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 19.7 19.7
Trusted cut-off 19.7 19.9
Noise cut-off 19.6 19.6
Model length: 169
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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

Selections

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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 RHD_DNA_bind domain has been found. There are 91 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
A0A0G2JTY4 View 3D Structure Click here
A0A0R4IIR4 View 3D Structure Click here
A0A0R4IN79 View 3D Structure Click here
A0A2R8RKG0 View 3D Structure Click here
A0A2R8S050 View 3D Structure Click here
A8JUV3 View 3D Structure Click here
B3DHW2 View 3D Structure Click here
D3Z9H7 View 3D Structure Click here
D3ZE20 View 3D Structure Click here
D3ZGB1 View 3D Structure Click here
D4A0I8 View 3D Structure Click here
D4A8H1 View 3D Structure Click here
E7F059 View 3D Structure Click here
E7F069 View 3D Structure Click here
E7F9Z5 View 3D Structure Click here
E7FE12 View 3D Structure Click here
F1QMI6 View 3D Structure Click here
F1QUZ9 View 3D Structure Click here
F1QXN5 View 3D Structure Click here
O88942 View 3D Structure Click here
O94916 View 3D Structure Click here
O95644 View 3D Structure Click here
P15307 View 3D Structure Click here
P15330 View 3D Structure Click here
P19838 View 3D Structure Click here
P25799 View 3D Structure Click here
P97305 View 3D Structure Click here
P98149 View 3D Structure Click here
Q00653 View 3D Structure Click here
Q01201 View 3D Structure Click here
Q04206 View 3D Structure Click here
Q04207 View 3D Structure Click here
Q04863 View 3D Structure Click here
Q04864 View 3D Structure Click here
Q0II00 View 3D Structure Click here
Q12968 View 3D Structure Click here
Q13469 View 3D Structure Click here
Q14934 View 3D Structure Click here
Q5U2Z4 View 3D Structure Click here
Q60591 View 3D Structure Click here
Q6DGE6 View 3D Structure Click here
Q7TQN4 View 3D Structure Click here
Q8K120 View 3D Structure Click here
Q94527 View 3D Structure Click here
Q9WTK5 View 3D Structure Click here
Q9WV30 View 3D Structure Click here
X1WEK5 View 3D Structure Click here