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124  structures 412  species 0  interactions 5487  sequences 131  architectures

Family: RHD_dimer (PF16179)

Summary: Rel homology dimerisation 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 dimerisation domain Provide feedback

The Rel homology domain (RHD) is composed of two structural domains, an N-terminal DNA_binding domain (PF00554) and a C-terminal dimerisation domain. This is the dimerisation domain [1].

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


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR032397

The Rel homology domain (RHD) is composed of two structural domains, an N-terminal DNA-binding domain ( INTERPRO ) and a C-terminal dimerisation domain. This is the dimerisation domain [ PUBMED:17869269 ].

This domain can be found in both nuclear factor of activated T cells (NFAT) and nuclear factor kappa-B (NFkB), which are RHD-containing transcription factors [ PUBMED:11344309 ].

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 E-set (CL0159), which has the following description:

This clan includes a diverse range of domains that have an Ig-like fold and appear to be distantly related to each other. The clan includes: PKD domains, cadherins and several families of bacterial Ig-like domains as well as viral tail fibre proteins. it also includes several Fibronectin type III domain-containing families.

The clan contains the following 257 members:

A2M A2M_BRD A2M_recep AA9 Adeno_GP19K AlcCBM31 Alpha-amylase_N Alpha_adaptinC2 Alpha_E2_glycop Anth_Ig aRib Arylsulfotran_N ASF1_hist_chap ATG19 BACON BACON_2 BatD BIg21 Big_1 Big_10 Big_11 Big_12 Big_13 Big_14 Big_15 Big_2 Big_3 Big_3_2 Big_3_3 Big_3_4 Big_3_5 Big_4 Big_5 Big_6 Big_7 Big_8 Big_9 Bile_Hydr_Trans BiPBP_C bMG1 bMG10 bMG3 bMG5 bMG6 BslA BsuPI Cadherin Cadherin-like Cadherin_2 Cadherin_3 Cadherin_4 Cadherin_5 Cadherin_pro CagX Calx-beta Candida_ALS_N CARDB CBM39 CBM_X2 CD45 CelD_N Ceramidse_alk_C CHB_HEX_C CHB_HEX_C_1 ChitinaseA_N ChiW_Ig_like Chlam_OMP6 CHU_C Coatamer_beta_C COP-gamma_platf CopC CshA_repeat Cyc-maltodext_N Cytomega_US3 DBB DsbC DUF11 DUF1410 DUF1425 DUF2271 DUF3244 DUF3458 DUF3501 DUF3823_C DUF3859 DUF4165 DUF4179 DUF4426 DUF4469 DUF4625 DUF4784_N DUF4879 DUF4959 DUF4982 DUF4998 DUF5001 DUF5008 DUF5011 DUF5060 DUF5065 DUF5103 DUF5115 DUF525 DUF5643 DUF6383 DUF6595 DUF916 EB_dh ECD Enterochelin_N EpoR_lig-bind ERAP1_C EstA_Ig_like Expansin_C Filamin FixG_C Flavi_glycop_C FlgD_ig fn3 Fn3-like fn3_2 fn3_4 fn3_5 fn3_6 FN3_7 Fn3_assoc fn3_PAP GBS_Bsp-like GlgE_dom_N_S Glucodextran_B Glyco_hydro2_C5 Glyco_hydro_2 Gmad2 GMP_PDE_delta GO-like_E_set GspA_SrpA_N Hanta_G1 He_PIG HECW_N HemeBinding_Shp Hemocyanin_C Herpes_BLLF1 HYR IalB IFNGR1 Ig_GlcNase Ig_mannosidase IL12p40_C Il13Ra_Ig IL17R_fnIII_D1 IL17R_fnIII_D2 IL2RB_N1 IL3Ra_N IL4Ra_N IL6Ra-bind Inhibitor_I42 Inhibitor_I71 InlK_D3 Integrin_alpha2 Interfer-bind Invasin_D3 IRK_C IrmA Iron_transport Kre9_KNH LacZ_4 LEA_2 Lep_receptor_Ig LIFR_D2 LIFR_N Lipase_bact_N LodA_N LPMO_10 LRR_adjacent LTD MALT1_Ig Mannosidase_ig MetallophosC MG1 MG2 MG3 MG4 Mo-co_dimer N_BRCA1_IG Na_K-ATPase NAR2 NDNF NDNF_C NEAT Neocarzinostat Neurexophilin NPCBM_assoc Omp28 PapD_C PBP-Tp47_c Peptidase_C25_C Phlebo_G2_C PhoD_N PKD PKD_2 PKD_3 PKD_4 PKD_5 PKD_6 Por_Secre_tail Pox_vIL-18BP Psg1 PTP_tm Pullulanase_N2 Pur_ac_phosph_N Qn_am_d_aIII Qn_am_d_aIV RabGGT_insert Reeler REJ RET_CLD1 RET_CLD3 RET_CLD4 RGI_lyase RHD_dimer Rho_GDI Rib RibLong SCAB-Ig SKICH SLAM SoxZ SprB SusE SVA SWM_repeat T2SS-T3SS_pil_N Tafi-CsgC TarS_C1 TcA_RBD TcfC TIG TIG_2 TIG_plexin TIG_SUH Tissue_fac Top6b_C TPPII TQ Transglut_C Transglut_N TRAP_beta TraQ_transposon UL16 Velvet WIF Wzt_C Y_Y_Y YBD YscW ZirS_C Zona_pellucida

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
(48)
Full
(5487)
Representative proteomes UniProt
(9406)
RP15
(480)
RP35
(1443)
RP55
(3894)
RP75
(5539)
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PP/heatmap 1            

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

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

Format an alignment

  Seed
(48)
Full
(5487)
Representative proteomes UniProt
(9406)
RP15
(480)
RP35
(1443)
RP55
(3894)
RP75
(5539)
Alignment:
Format:
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Sequence:
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Download options

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
(48)
Full
(5487)
Representative proteomes UniProt
(9406)
RP15
(480)
RP35
(1443)
RP55
(3894)
RP75
(5539)
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: Jackhmmer:Q04863
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Eberhardt R
Number in seed: 48
Number in full: 5487
Average length of the domain: 99.00 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 11.26 %

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 28.3 28.3
Trusted cut-off 28.3 28.3
Noise cut-off 28.2 28.2
Model length: 103
Family (HMM) version: 8
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

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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_dimer 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
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
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