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15  structures 1006  species 7  interactions 1143  sequences 26  architectures

Family: Med6 (PF04934)

Summary: MED6 mediator sub complex component

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 "MED6". More...

MED6 Edit Wikipedia article

MED6
Identifiers
AliasesMED6, ARC33, NY-REN-28, mediator complex subunit 6
External IDsOMIM: 602984 MGI: 1917042 HomoloGene: 3990 GeneCards: MED6
Gene location (Human)
Chromosome 14 (human)
Chr.Chromosome 14 (human)[1]
Chromosome 14 (human)
Genomic location for MED6
Genomic location for MED6
Band14q24.2Start70,581,257 bp[1]
End70,600,690 bp[1]
RNA expression pattern
PBB GE MED6 210104 at fs.png

PBB GE MED6 207079 s at fs.png
More reference expression data
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_005466
NM_001284209
NM_001284210
NM_001284211

NM_027213
NM_001347384
NM_001347385
NM_001347386

RefSeq (protein)

NP_001271138
NP_001271139
NP_001271140
NP_005457

NP_001334313
NP_001334314
NP_001334315

Location (UCSC)Chr 14: 70.58 – 70.6 MbChr 12: 81.57 – 81.6 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse
Med6
Identifiers
SymbolMed6
PfamPF04934
InterProIPR007018

Mediator of RNA polymerase II transcription subunit 6 is one of the subunits of the Mediator complex. It is an enzyme that in humans is encoded by the MED6 gene.[5][6][7]

Protein family

This family of proteins represent the transcriptional mediator protein subunit 6 that is required for activation of many RNA polymerase II promoters and which are conserved from yeast to humans.[5]

Interactions

MED6 has been shown to interact with:

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000133997 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000002679 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ a b Lee YC, Min S, Gim BS, Kim YJ (August 1997). "A transcriptional mediator protein that is required for activation of many RNA polymerase II promoters and is conserved from yeast to humans". Mol. Cell. Biol. 17 (8): 4622–32. doi:10.1128/MCB.17.8.4622. PMC 232315. PMID 9234719.
  6. ^ Jiang YW, Veschambre P, Erdjument-Bromage H, Tempst P, Conaway JW, Conaway RC, Kornberg RD (Aug 1998). "Mammalian mediator of transcriptional regulation and its possible role as an end-point of signal transduction pathways". Proc Natl Acad Sci U S A. 95 (15): 8538–8543. doi:10.1073/pnas.95.15.8538. PMC 21111. PMID 9671713.
  7. ^ "Entrez Gene: MED6 mediator of RNA polymerase II transcription, subunit 6 homolog (S. cerevisiae)".
  8. ^ Yang F, DeBeaumont R, Zhou S, Näär AM (Feb 2004). "The activator-recruited cofactor/Mediator coactivator subunit ARC92 is a functionally important target of the VP16 transcriptional activator". Proc. Natl. Acad. Sci. U.S.A. 101 (8): 2339–44. doi:10.1073/pnas.0308676100. PMC 356952. PMID 14983011.
  9. ^ Wang G, Cantin GT, Stevens JL, Berk AJ (Jul 2001). "Characterization of mediator complexes from HeLa cell nuclear extract". Mol. Cell. Biol. 21 (14): 4604–13. doi:10.1128/MCB.21.14.4604-4613.2001. PMC 87123. PMID 11416138.
  10. ^ a b Ito M, Yuan CX, Malik S, Gu W, Fondell JD, Yamamura S, Fu ZY, Zhang X, Qin J, Roeder RG (Mar 1999). "Identity between TRAP and SMCC complexes indicates novel pathways for the function of nuclear receptors and diverse mammalian activators". Mol. Cell. 3 (3): 361–70. doi:10.1016/s1097-2765(00)80463-3. PMID 10198638.
  11. ^ a b Kang YK, Guermah M, Yuan CX, Roeder RG (Mar 2002). "The TRAP/Mediator coactivator complex interacts directly with estrogen receptors alpha and beta through the TRAP220 subunit and directly enhances estrogen receptor function in vitro". Proc. Natl. Acad. Sci. U.S.A. 99 (5): 2642–7. doi:10.1073/pnas.261715899. PMC 122401. PMID 11867769.
  12. ^ Sun X, Zhang Y, Cho H, Rickert P, Lees E, Lane W, Reinberg D (Aug 1998). "NAT, a human complex containing Srb polypeptides that functions as a negative regulator of activated transcription". Mol. Cell. 2 (2): 213–22. doi:10.1016/s1097-2765(00)80131-8. PMID 9734358.

Further reading

  • Maruyama K, Sugano S (1994). "Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides". Gene. 138 (1–2): 171–174. doi:10.1016/0378-1119(94)90802-8. PMID 8125298.
  • Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, Suyama A, Sugano S (1997). "Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library". Gene. 200 (1–2): 149–156. doi:10.1016/S0378-1119(97)00411-3. PMID 9373149.
  • Sun X, Zhang Y, Cho H, Rickert P, Lees E, Lane W, Reinberg D (1998). "NAT, a human complex containing Srb polypeptides that functions as a negative regulator of activated transcription". Mol. Cell. 2 (2): 213–222. doi:10.1016/S1097-2765(00)80131-8. PMID 9734358.
  • Gu W, Malik S, Ito M, Yuan CX, Fondell JD, Zhang X, Martinez E, Qin J, Roeder RG (1999). "A novel human SRB/MED-containing cofactor complex, SMCC, involved in transcription regulation". Mol. Cell. 3 (1): 97–108. doi:10.1016/S1097-2765(00)80178-1. PMID 10024883.
  • Ito M, Yuan CX, Malik S, Gu W, Fondell JD, Yamamura S, Fu ZY, Zhang X, Qin J, Roeder RG (1999). "Identity between TRAP and SMCC complexes indicates novel pathways for the function of nuclear receptors and diverse mammalian activators". Mol. Cell. 3 (3): 361–370. doi:10.1016/S1097-2765(00)80463-3. PMID 10198638.
  • Rachez C, Lemon BD, Suldan Z, Bromleigh V, Gamble M, Näär AM, Erdjument-Bromage H, Tempst P, Freedman LP (1999). "Ligand-dependent transcription activation by nuclear receptors requires the DRIP complex". Nature. 398 (6730): 824–828. doi:10.1038/19783. PMID 10235266.
  • Näär AM, Beaurang PA, Zhou S, Abraham S, Solomon W, Tjian R (1999). "Composite co-activator ARC mediates chromatin-directed transcriptional activation". Nature. 398 (6730): 828–832. doi:10.1038/19789. PMID 10235267.
  • Scanlan MJ, Gordan JD, Williamson B, Stockert E, Bander NH, Jongeneel V, Gure AO, Jäger D, Jäger E, Knuth A, Chen YT, Old LJ (1999). "Antigens recognized by autologous antibody in patients with renal-cell carcinoma". Int. J. Cancer. 83 (4): 456–464. doi:10.1002/(SICI)1097-0215(19991112)83:4<456::AID-IJC4>3.0.CO;2-5. PMID 10508479.
  • Ge K, Guermah M, Yuan CX, Ito M, Wallberg AE, Spiegelman BM, Roeder RG (2002). "Transcription coactivator TRAP220 is required for PPAR gamma 2-stimulated adipogenesis". Nature. 417 (6888): 563–567. doi:10.1038/417563a. PMID 12037571.
  • Kato Y, Habas R, Katsuyama Y, Näär AM, He X (2002). "A component of the ARC/Mediator complex required for TGF beta/Nodal signalling". Nature. 418 (6898): 641–646. doi:10.1038/nature00969. PMID 12167862.
  • Sato S, Tomomori-Sato C, Banks CA, Sorokina I, Parmely TJ, Kong SE, Jin J, Cai Y, Lane WS, Brower CS, Conaway RC, Conaway JW (2003). "Identification of mammalian Mediator subunits with similarities to yeast Mediator subunits Srb5, Srb6, Med11, and Rox3". J. Biol. Chem. 278 (17): 15123–15127. doi:10.1074/jbc.C300054200. PMID 12584197.
  • Sato S, Tomomori-Sato C, Banks CA, Parmely TJ, Sorokina I, Brower CS, Conaway RC, Conaway JW (2004). "A mammalian homolog of Drosophila melanogaster transcriptional coactivator intersex is a subunit of the mammalian Mediator complex". J. Biol. Chem. 278 (50): 49671–49674. doi:10.1074/jbc.C300444200. PMID 14576168.
  • Tomomori-Sato C, Sato S, Parmely TJ, Banks CA, Sorokina I, Florens L, Zybailov B, Washburn MP, Brower CS, Conaway RC, Conaway JW (2004). "A mammalian mediator subunit that shares properties with Saccharomyces cerevisiae mediator subunit Cse2". J. Biol. Chem. 279 (7): 5846–5851. doi:10.1074/jbc.M312523200. PMID 14638676.
  • Yang F, DeBeaumont R, Zhou S, Näär AM (2004). "The activator-recruited cofactor/Mediator coactivator subunit ARC92 is a functionally important target of the VP16 transcriptional activator". Proc. Natl. Acad. Sci. U.S.A. 101 (8): 2339–2344. doi:10.1073/pnas.0308676100. PMC 356952. PMID 14983011.
  • Sato S, Tomomori-Sato C, Parmely TJ, Florens L, Zybailov B, Swanson SK, Banks CA, Jin J, Cai Y, Washburn MP, Conaway JW, Conaway RC (2004). "A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology". Mol. Cell. 14 (5): 685–691. doi:10.1016/j.molcel.2004.05.006. PMID 15175163.
  • Pavri R, Lewis B, Kim TK, Dilworth FJ, Erdjument-Bromage H, Tempst P, de Murcia G, Evans R, Chambon P, Reinberg D (2005). "PARP-1 determines specificity in a retinoid signaling pathway via direct modulation of mediator". Mol. Cell. 18 (1): 83–96. doi:10.1016/j.molcel.2005.02.034. PMID 15808511.

External links

This article incorporates text from the public domain Pfam and InterPro: IPR007018


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.

MED6 mediator sub complex component Provide feedback

Component of RNA polymerase II holoenzyme and mediator sub complex.

Literature references

  1. Kim YJ, Bjorklund S, Li Y, Sayre MH, Kornberg RD; , Cell 1994;77:599-608.: A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. PUBMED:8187178 EPMC:8187178

  2. Lee YC, Min S, Gim BS, Kim YJ; , Mol Cell Biol 1997;17:4622-4632.: A transcriptional mediator protein that is required for activation of many RNA polymerase II promoters and is conserved from yeast to humans. PUBMED:9234719 EPMC:9234719

  3. Spahr H, Samuelsen CO, Baraznenok V, Ernest I, Huylebroeck D, Remacle JE, Samuelsson T, Kieselbach T, Holmberg S, Gustafsson CM; , Proc Natl Acad Sci U S A 2001;98:11985-11990.: Analysis of Schizosaccharomyces pombe mediator reveals a set of essential subunits conserved between yeast and metazoan cells. PUBMED:11572939 EPMC:11572939


This tab holds annotation information from the InterPro database.

InterPro entry IPR007018

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.

Regulation of mRNA synthesis requires intermediary proteins that transduce regulatory signals from upstream transcriptional activator proteins to basal transcription machinery at the core promoter. Three types of intermediary factors that enable the basal transcription machinery to respond to transcriptional activator proteins bound to regulatory DNA sequences have been identified: (i) TAFIIs, which associate with TATA-binding protein (TBP) to form TFIID; (ii) mediator, which associates with RNA polymerase II to form a holo-polymerase; and (iii) coactivators such as human upstream stimulatory activity (USA), mammalian CBP/P300, yeast ADA complex, and HMG proteins. The interaction of these multiprotein complexes with activators and general transcription factors is essential for transcriptional regulation.

This family of proteins represent the transcriptional mediator protein subunit 6 that is required for activation of many RNA polymerase II promoters and which are conserved from yeast to humans [PUBMED:9234719].

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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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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(129)
Full
(1143)
Representative proteomes UniProt
(1618)
NCBI
(1834)
Meta
(2)
RP15
(307)
RP35
(602)
RP55
(856)
RP75
(1071)
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  Seed
(129)
Full
(1143)
Representative proteomes UniProt
(1618)
NCBI
(1834)
Meta
(2)
RP15
(307)
RP35
(602)
RP55
(856)
RP75
(1071)
Alignment:
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  Seed
(129)
Full
(1143)
Representative proteomes UniProt
(1618)
NCBI
(1834)
Meta
(2)
RP15
(307)
RP35
(602)
RP55
(856)
RP75
(1071)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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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.

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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_4045 (release 7.6)
Previous IDs: MED6;
Type: Family
Sequence Ontology: SO:0100021
Author: Wood V , Bateman A
Number in seed: 129
Number in full: 1143
Average length of the domain: 136.90 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 47.82 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.2 20.2
Trusted cut-off 20.3 21.1
Noise cut-off 19.9 19.3
Model length: 133
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Interactions

There are 7 interactions for this family. More...

Med22 Med8 Med17 Med17 RNA_pol_Rpb1_R Med22 Med8

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 Med6 domain has been found. There are 15 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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