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3  structures 1066  species 0  interactions 1190  sequences 19  architectures

Family: Med4 (PF10018)

Summary: Vitamin-D-receptor interacting Mediator subunit 4

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This is the Wikipedia entry entitled "MED4". More...

MED4 Edit Wikipedia article

MED4
Identifiers
Aliases MED4, ARC36, DRIP36, HSPC126, TRAP36, VDRIP, mediator complex subunit 4
External IDs MGI: 1914631 HomoloGene: 8568 GeneCards: MED4
Gene location (Human)
Chromosome 13 (human)
Chr. Chromosome 13 (human)[1]
Chromosome 13 (human)
Genomic location for MED4
Genomic location for MED4
Band 13q14.2 Start 48,053,323 bp[1]
End 48,095,131 bp[1]
RNA expression pattern
PBB GE MED4 217843 s at fs.png
More reference expression data
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_014166
NM_001270629

NM_026119

RefSeq (protein)

NP_001257558
NP_054885

NP_080395

Location (UCSC) Chr 13: 48.05 – 48.1 Mb Chr 13: 73.51 – 73.52 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse
Med4
Identifiers
Symbol Med4
Pfam PF10018
InterPro IPR019258

Mediator of RNA polymerase II transcription subunit 4 also known as mediator complex subunit 4 (MED4), a component of Mediator or vitamin D3 receptor-interacting protein complex 36 kDa component (DRIP36) is a protein that in humans is encoded by the MED4 gene.[5][6][7]

Function

The protein encoded by this gene is a component of the vitamin D receptor-interacting protein (DRIP) complex which functions as a nuclear receptor coactivator. The DRIP complex is capable of activating nuclear receptors in a ligand-dependent manner.[6]

Interactions

MED4 has been shown to interact with MED25.[8]

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000136146 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000022109 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". 
  4. ^ "Mouse PubMed Reference:". 
  5. ^ "Entrez Gene: MED4 mediator of RNA polymerase II transcription, subunit 4 homolog (S. cerevisiae)". 
  6. ^ a b Rachez C, Lemon BD, Suldan Z, Bromleigh V, Gamble M, Näär AM, Erdjument-Bromage H, Tempst P, Freedman LP (April 1999). "Ligand-dependent transcription activation by nuclear receptors requires the DRIP complex". Nature. 398 (6730): 824–8. PMID 10235266. doi:10.1038/19783. 
  7. ^ Zhang QH, Ye M, Wu XY, Ren SX, Zhao M, Zhao CJ, Fu G, Shen Y, Fan HY, Lu G, Zhong M, Xu XR, Han ZG, Zhang JW, Tao J, Huang QH, Zhou J, Hu GX, Gu J, Chen SJ, Chen Z (October 2000). "Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells". Genome Research. 10 (10): 1546–60. PMC 310934Freely accessible. PMID 11042152. doi:10.1101/gr.140200. 
  8. ^ Tomomori-Sato C, Sato S, Parmely TJ, Banks CA, Sorokina I, Florens L, Zybailov B, Washburn MP, Brower CS, Conaway RC, Conaway JW (Feb 2004). "A mammalian mediator subunit that shares properties with Saccharomyces cerevisiae mediator subunit Cse2". J. Biol. Chem. 279 (7): 5846–51. PMID 14638676. doi:10.1074/jbc.M312523200. 

Further reading


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

This is the Wikipedia entry entitled "Mediator (coactivator)". More...

Mediator (coactivator) Edit Wikipedia article

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.

Vitamin-D-receptor interacting Mediator subunit 4 Provide feedback

Members of this family function as part of the Mediator (Med) complex, which links DNA-bound transcriptional regulators and the general transcription machinery, particularly the RNA polymerase II enzyme. They play a role in basal transcription by mediating activation or repression according to the specific complement of transcriptional regulators bound to the promoter [1].

Literature references

  1. Rachez C, Lemon BD, Suldan Z, Bromleigh V, Gamble M, Naar AM, Erdjument-Bromage H, Tempst P, Freedman LP; , Nature. 1999;398:824-828.: Ligand-dependent transcription activation by nuclear receptors requires the DRIP complex. PUBMED:10235266 EPMC:10235266

  2. Naar AM, Beaurang PA, Zhou S, Abraham S, Solomon W, Tjian R; , Nature. 1999;398:828-832.: Composite co-activator ARC mediates chromatin-directed transcriptional activation. PUBMED:10235267 EPMC:10235267

  3. Bourbon HM, Aguilera A, Ansari AZ, Asturias FJ, Berk AJ, Bjorklund S, Blackwell TK, Borggrefe T, Carey M, Carlson M, Conaway JW, Conaway RC, Emmons SW, Fondell JD, Freedman LP, Fukasawa T, Gustafsson CM, Han M, He X, Herman PK, Hinnebusch AG, Holmberg S, , Mol Cell. 2004;14:553-557.: A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. PUBMED:15175151 EPMC:15175151


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR019258

The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.

The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11.

The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation.

  • The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22.
  • The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4.
  • The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16.
  • The CDK8 module contains: MED12, MED13, CCNC and CDK8.

Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.

Members of this family represent the Med4 subunit of the Mediator (Med) complex [PUBMED:10235266, PUBMED:10235267].

Gene Ontology

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

Domain organisation

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Alignments

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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
(14)
Full
(1190)
Representative proteomes UniProt
(1853)
NCBI
(2194)
Meta
(0)
RP15
(199)
RP35
(523)
RP55
(849)
RP75
(1203)
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Key: ✓ available, x not generated, not available.

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  Seed
(14)
Full
(1190)
Representative proteomes UniProt
(1853)
NCBI
(2194)
Meta
(0)
RP15
(199)
RP35
(523)
RP55
(849)
RP75
(1203)
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
(14)
Full
(1190)
Representative proteomes UniProt
(1853)
NCBI
(2194)
Meta
(0)
RP15
(199)
RP35
(523)
RP55
(849)
RP75
(1203)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   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: KOGs (KOG4552)
Previous IDs: VDRIP;
Type: Family
Sequence Ontology: SO:0100021
Author: KOGs, Finn RD , Sammut SJ
Number in seed: 14
Number in full: 1190
Average length of the domain: 192.60 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 62.24 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.5 25.5
Trusted cut-off 25.5 25.5
Noise cut-off 25.4 25.4
Model length: 194
Family (HMM) version: 10
Download: download the raw HMM for this family

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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 Med4 domain has been found. There are 3 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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