The domain within your query sequence starts at position 1675 and ends at position 2197; the E-value for the Med13_C domain shown below is 1e-142.

VIYMVDPFTYTAEEDSSSGNFWLLSLMRCYTEMLDHLPEHMRSSFILQIVPCQYMLQTMK
DEHVFYIQYLKSMAFSVYCQCRRPLPTQIHIKSLTGFGPAASIEMTLKNPERPSPIQLYS
PPFILAPIKDKQTEPGETFGEASQKYNVLFVGYCLSHDQRWLLASCTDLHGELLETCVVN
IALPSRSRKSKVSARKVGLQKLWEWCLGIVQMTSLPWRVVIGRLGRLGHGELKDWSILLG
ECSLQTISKQLKDVCRMCGISAADSPSILSACLVAMEPQGSFVVMPDAVTMGSVFGRSTA
LNMQSSQLNTPQDASCTHILVFPTSSTIQVAPANYPNEDGFSPNNDDMFVDLPFPDDMDN
DIGILMTGNLHSSPNSSPVPSPGSPSGIGVGSHFQHSRSQGERLLSREAPEELKQQPLAL
GYFVSTAKAENLPQWFWSSCPQARNQCPLFLKASLHHHISVAQTDELLPARTSQRAPHPL
DSKTTSDVLRFVLEQYNALSWLTCNPATQDRTSCLPVHFVVLT

Med13_C

• PFAM accession number: PF06333
• Interpro abstract (IPR009401):

  This entry represents the C-terminal domain of Med13. This domain is also identified as an RNaseH domain of the medPIWI PIWI/Argonaute module. medPIWI is the core domain found in the Med13 protein. The medPIWI module in Med13 is predicted to bind double-stranded nucleic acids, triggering the experimentally-observed conformational switch in the CDK8 subcomplex which regulates the Mediator complex [ (PUBMED:23758928) ]. Med13 is a component of the SRB8-11 complex. The SRB8-11 complex is a regulatory module of the Mediator complex, which may be involved in the transcriptional repression of a subset of genes regulated by Mediator. It acts by inhibiting the association of the Mediator complex with RNA polymerase II to form the holoenzyme complex [ (PUBMED:12738880) ].

  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.

• GO process: regulation of transcription by RNA polymerase II (GO:0006357)
• GO component: mediator complex (GO:0016592)
• GO function: transcription coregulator activity (GO:0003712)

This is a PFAM domain. For full annotation and more information, please see the PFAM entry Med13_C