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0  structures 342  species 0  interactions 352  sequences 4  architectures

Family: Med9 (PF07544)

Summary: RNA polymerase II transcription mediator complex subunit 9

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RNA polymerase II transcription mediator complex subunit 9 Provide feedback

This family of Med9 proteins is conserved in yeasts. It forms part of the middle region of Mediator [4]. Med9 has two functional domains. The species-specific amino-terminal half (aa 1-63) plays a regulatory role in transcriptional regulation, whereas this well-conserved carboxy-terminal half (aa 64-149) has a more fundamental function involved in direct binding to the amino-terminal portions of Med4 and Med7 and the assembly of Med9 into the Middle module. Also, some unidentified factor(s) in med9 extracts may impact the binding of TFIID to the promoter [5].

Literature references

  1. 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; , J Biol Chem 2003;278:15123-15127.: Identification of mammalian Mediator subunits with similarities to yeast Mediator subunits Srb5, Srb6, Med11, and Rox3. PUBMED:12584197 EPMC:12584197

  2. Sato S, Tomomori-Sato C, Banks CA, Parmely TJ, Sorokina I, Brower CS, Conaway RC, Conaway JW; , J Biol Chem 2003;278:49671-49674.: A mammalian homolog of Drosophila melanogaster transcriptional coactivator intersex is a subunit of the mammalian Mediator complex. PUBMED:14576168 EPMC:14576168

  3. Xiao Z, McGrew JT, Schroeder AJ, Fitzgerald-Hayes M; , Mol Cell Biol 1993;13:4691-4702.: CSE1 and CSE2, two new genes required for accurate mitotic chromosome segregation in Saccharomyces cerevisiae. PUBMED:8336709 EPMC:8336709

  4. 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

  5. Takahashi H, Kasahara K, Kokubo T;, Genes Cells. 2009;14:53-67.: Saccharomyces cerevisiae Med9 comprises two functionally distinct domains that play different roles in transcriptional regulation. PUBMED:19077037 EPMC:19077037


This tab holds annotation information from the InterPro database.

InterPro entry IPR011425

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.

This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex [PUBMED:19077037]; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme.

Med9 alternatively known as the chromosome segregation protein, CSE2 (SWISSPROT) is required, along with CSE1 (SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [PUBMED:8336709].

Gene Ontology

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(65)
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(629)
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RP35
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RP55
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RP75
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  Seed
(65)
Full
(352)
Representative proteomes UniProt
(691)
NCBI
(629)
Meta
(0)
RP15
(67)
RP35
(160)
RP55
(251)
RP75
(345)
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  Seed
(65)
Full
(352)
Representative proteomes UniProt
(691)
NCBI
(629)
Meta
(0)
RP15
(67)
RP35
(160)
RP55
(251)
RP75
(345)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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Curation View help on the curation process

Seed source: Pfam-B_45625 (release 11.0)
Previous IDs: CSE2;
Type: Family
Author: Wood V, Studholme DJ
Number in seed: 65
Number in full: 352
Average length of the domain: 81.60 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 50.95 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.9 26.9
Trusted cut-off 27.1 27.2
Noise cut-off 26.7 26.8
Model length: 80
Family (HMM) version: 11
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