2XNF

The Mediator Med25 activator interaction domain: Structure and cooperative binding of VP16 subdomains

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	SPOC domain-like	8092967	3000675	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Med25	e2xnfA1	A: beta barrels	X: SPOC domain-like	H: SPOC domain-related	T: SPOC domain	F: Med25	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.290.30	Mainly Beta	Beta Barrel	Ku70	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF11232	Mediator complex subunit 25 PTOV activation and synapsin 2 (Med25)	Mediator complex subunit 25 PTOV activation and synapsin 2	Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [1-2]. It is arranged into four different sections, a core, a head, a tail a ...	Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function [4]. The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This family is the combined PTOV and SD2 domains. the PTOV domain being the domain through which Med25 co-operates with the histone acetyltransferase CBP, but the function of the SD2 domain is unclear [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 25	transcription factor binding transcription coregulator binding protein binding binding transcription coactivator binding nuclear retinoic acid receptor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding nuclear retinoid X receptor binding DNA-binding transcription factor binding	regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription positive regulation of metabolic process regulation of DNA-templated transcription initiation regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription positive regulation of metabolic process regulation of DNA-templated transcription initiation regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process transcription initiation at RNA polymerase II promoter positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription initiation by RNA polymerase II biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression positive regulation of transcription by RNA polymerase II macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation positive regulation of DNA-templated transcription initiation positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of transcription initiation by RNA polymerase II metabolic process cellular process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process transcription preinitiation complex assembly cellular component organization cellular component biogenesis protein-DNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis protein-containing complex organization protein-DNA complex assembly RNA polymerase II preinitiation complex assembly negative regulation of cell population proliferation fibroblast proliferation cell population proliferation negative regulation of biological process regulation of fibroblast proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of fibroblast proliferation transcription elongation by RNA polymerase II positive regulation of transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription, elongation regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II DNA-templated transcription elongation negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process positive regulation of chromatin binding regulation of molecular function positive regulation of molecular function regulation of binding regulation of chromatin binding positive regulation of binding positive regulation of mediator complex assembly regulation of cellular component organization positive regulation of cellular component organization positive regulation of cellular component biogenesis regulation of mediator complex assembly regulation of cellular component biogenesis mediator complex assembly regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure core mediator complex nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle mediator complex membrane-enclosed lumen RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure core mediator complex nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle mediator complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
A	IPR021397	Mediator complex, subunit Med25, synapsin 1	Domain
A	IPR021419	Mediator of RNA polymerase II transcription subunit 25, von Willebrand factor type A domain	Domain
A	IPR038196	Mediator complex subunit 25, PTOV domain superfamily	Homologous Superfamily
A	IPR021394	Mediator complex, subunit Med25, PTOV domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q71SY5	Charcot-Marie-Tooth disease congenital cataract-microcephaly-nevus flammeus simplex-severe intellectual disability syndrome Charcot-Marie-Tooth disease type 2B2 intellectual disability peripheral neuropathy Abnormality of the cornea neurodegenerative disease pancreatic intraductal papillary-mucinous neoplasm pituitary cancer osteosarcoma peripheral nervous system disease motor peripheral neuropathy ovarian cancer

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.