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30  structures 1073  species 0  interactions 1462  sequences 20  architectures

Family: Med18 (PF09637)

Summary: Med18 protein

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 "Mediator (coactivator)". More...

Mediator (coactivator) Edit Wikipedia article

Mediator is a multiprotein complex that functions as a transcriptional coactivator. It was discovered by Roger D. Kornberg, winner of the 2006 Nobel Prize in Chemistry. It is also referred to in scientific literature as the Vitamin D Receptor Interacting Protein (DRIP) coactivator complex and the Thyroid Hormone Receptor-associated Proteins (TRAP).

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.

Med18 protein Provide feedback

Med18 is one subunit of Mediator, a head-module multiprotein complex, that stimulates basal RNA polymerase II (Pol II) transcription. Med18 consists of an eight-stranded beta-barrel with a central pore and three flanking helices. It complexes with Med8 and Med20 proteins by forming a heterodimer of two-fold symmetry with Med20 and binding the C-terminal alpha-helix region of Med8 across the top of its barrel. This complex creates a multipartite TBP-binding site that can be modulated by transcriptional activators [1].

Literature references

  1. Lariviere L, Geiger S, Hoeppner S, Rother S, Strasser K, Cramer P; , Nat Struct Mol Biol. 2006;13:895-901.: Structure and TBP binding of the Mediator head subcomplex Med8-Med18-Med20. PUBMED:16964259 EPMC:16964259


This tab holds annotation information from the InterPro database.

InterPro entry IPR019095

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.

Med18 is one subunit of the Mediator complex and a component of the head module that is involved in stimulating basal RNA polymerase II (PolII) transcription. Med18 consists of an eight-stranded beta-barrel with a central pore and three flanking helices. It complexes with Med8 and Med20 proteins by forming a heterodimer of two-fold symmetry with Med20 and binding the C-terminal alpha-helix region of Med8 across the top of its barrel. This complex creates a multipartite TBP-binding site that can be modulated by transcriptional activators [ PUBMED:16964259 ].

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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Pfam Clan

This family is a member of clan CYTH (CL0273), which has the following description:

CyaB like adenylyl cyclase and the mammalian thiamine triphosphatases define a novel superfamily of catalytic domains called the CYTH domain that is present in all three superkingdoms of life. The catalytic core of these enzymes contain a novel alpha beta scaffold with 6 conserved acidic residues and 4 basic residues [1].

The clan contains the following 7 members:

CYTH Med18 Med20 mRNA_triPase Pox_ATPase-GT VTC Zwilch

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
(21)
Full
(1462)
Representative proteomes UniProt
(2422)
RP15
(302)
RP35
(637)
RP55
(1105)
RP75
(1492)
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PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(21)
Full
(1462)
Representative proteomes UniProt
(2422)
RP15
(302)
RP35
(637)
RP55
(1105)
RP75
(1492)
Alignment:
Format:
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Sequence:
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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
(21)
Full
(1462)
Representative proteomes UniProt
(2422)
RP15
(302)
RP35
(637)
RP55
(1105)
RP75
(1492)
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: pdb_2hzm
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 21
Number in full: 1462
Average length of the domain: 171 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 84.97 %

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 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 249
Family (HMM) version: 13
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

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 Med18 domain has been found. There are 30 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
A0A044V9R2 View 3D Structure Click here
A0A077ZFS9 View 3D Structure Click here
A0A0D2HNC7 View 3D Structure Click here
A0A0K0DW87 View 3D Structure Click here
A0A0N4UAA0 View 3D Structure Click here
A0A175WDB5 View 3D Structure Click here
A0A1C1CTP1 View 3D Structure Click here
A1CE73 View 3D Structure Click here
A1DM82 View 3D Structure Click here
A2RBB7 View 3D Structure Click here
A3LU54 View 3D Structure Click here
C0NGB7 View 3D Structure Click here
C1HAJ7 View 3D Structure Click here
G4VNG8 View 3D Structure Click here
J9B0R8 View 3D Structure Click here
M0R976 View 3D Structure Click here
O14198 View 3D Structure Click here
P32585 View 3D Structure Click here
Q0VCD4 View 3D Structure Click here
Q17IN5 View 3D Structure Click here
Q1E065 View 3D Structure Click here
Q28GE1 View 3D Structure Click here
Q2UMB8 View 3D Structure Click here
Q4WNC6 View 3D Structure Click here
Q54MR3 View 3D Structure Click here
Q59X40 View 3D Structure Click here
Q5B128 View 3D Structure Click here
Q61D43 View 3D Structure Click here
Q6BXL9 View 3D Structure Click here
Q6CDK1 View 3D Structure Click here
Q6CQQ0 View 3D Structure Click here
Q6FSU0 View 3D Structure Click here
Q75EI4 View 3D Structure Click here
Q7QGX9 View 3D Structure Click here
Q7T3H7 View 3D Structure Click here
Q966M5 View 3D Structure Click here
Q9BUE0 View 3D Structure Click here
Q9CZ82 View 3D Structure Click here
Q9XZT1 View 3D Structure Click here
U7Q8B7 View 3D Structure Click here