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0  structures 329  species 0  interactions 567  sequences 10  architectures

Family: Med30 (PF11315)

Summary: Mediator complex subunit 30

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 "MED30". More...

MED30 Edit Wikipedia article

MED30
Identifiers
Aliases MED30, MED30S, THRAP6, TRAP25, mediator complex subunit 30
External IDs MGI: 1917040 HomoloGene: 12329 GeneCards: MED30
Gene location (Human)
Chromosome 8 (human)
Chr. Chromosome 8 (human)[1]
Chromosome 8 (human)
Genomic location for MED30
Genomic location for MED30
Band n/a Start 117,520,713 bp[1]
End 117,540,262 bp[1]
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_001282986
NM_080651

NM_027212

RefSeq (protein)

NP_001269915
NP_542382

NP_081488

Location (UCSC) Chr 8: 117.52 – 117.54 Mb Chr 8: 52.71 – 52.73 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse
Med30
Identifiers
Symbol Med30
Pfam PF11315
InterPro IPR021019

Mediator of RNA polymerase II transcription subunit 30 is an enzyme that in humans is encoded by the MED30 gene.[5] It represents subunit Med30 of the Mediator complex and is metazoan-specific,[6] having no homologues in yeasts.

Interactions

MED30 has been shown to interact with MED22.[7]

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000164758 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000038622 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". 
  4. ^ "Mouse PubMed Reference:". 
  5. ^ "Entrez Gene: THRAP6 thyroid hormone receptor associated protein 6". 
  6. ^ Baek HJ, Malik S, Qin J, Roeder RG (Apr 2002). "Requirement of TRAP/mediator for both activator-independent and activator-dependent transcription in conjunction with TFIID-associated TAF(II)s". Molecular and Cellular Biology. 22 (8): 2842–52. PMC 133729Freely accessible. PMID 11909976. doi:10.1128/MCB.22.8.2842-2852.2002. 
  7. ^ 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 (Apr 2003). "Identification of mammalian Mediator subunits with similarities to yeast Mediator subunits Srb5, Srb6, Med11, and Rox3". The Journal of Biological Chemistry. 278 (17): 15123–7. PMID 12584197. doi:10.1074/jbc.C300054200. 

Further reading


This article incorporates text from the public domain Pfam and InterPro IPR021019

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.

Mediator complex subunit 30 Provide feedback

Med30 is a metazoan-specific subunit of Mediator, having no homologues in yeasts.

Literature references

  1. 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

  2. Baek HJ, Malik S, Qin J, Roeder RG; , Mol Cell Biol. 2002;22:2842-2852.: Requirement of TRAP/mediator for both activator-independent and activator-dependent transcription in conjunction with TFIID-associated TAF(II)s. PUBMED:11909976 EPMC:11909976


This tab holds annotation information from the InterPro database.

InterPro entry IPR021019

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.

Med30 is a metazoan-specific subunit of Mediator [ PUBMED:11909976 ], having no homologues in yeasts.

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 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
(12)
Full
(567)
Representative proteomes UniProt
(938)
RP15
(96)
RP35
(211)
RP55
(479)
RP75
(644)
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Key: ✓ available, x not generated, not available.

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  Seed
(12)
Full
(567)
Representative proteomes UniProt
(938)
RP15
(96)
RP35
(211)
RP55
(479)
RP75
(644)
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  Seed
(12)
Full
(567)
Representative proteomes UniProt
(938)
RP15
(96)
RP35
(211)
RP55
(479)
RP75
(644)
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: Pfam-B_28118 (release 23.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 12
Number in full: 567
Average length of the domain: 125.80 aa
Average identity of full alignment: 52 %
Average coverage of the sequence by the domain: 51.65 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.1 28.1
Trusted cut-off 28.1 28.4
Noise cut-off 27.8 27.8
Model length: 147
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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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
A0A0G2JWW8 View 3D Structure Click here
Q4V8V8 View 3D Structure Click here
Q6PC45 View 3D Structure Click here
Q96HR3 View 3D Structure Click here
Q9CQI9 View 3D Structure Click here
Q9W0P3 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;