2XNF: PDB entry 2XNF

The Mediator Med25 activator interaction domain: Structure and cooperative binding of VP16 subdomains. Determined by solution NMR. Released 9 Mar 2011.

Method: Solution NMR
Organism: HOMO SAPIENS
Chains: 1
Atoms: 1,284
Mol. weight: 18.28 kDa
Released: 9 Mar 2011

Explore 2XNF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2XNF contains 6 α-helices and 7 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	399-409	11	1
β-strand	424-434	11	1
α-helix	441-443	3
β-strand	447-454	8	1
α-helix	455-458	4
α-helix	459-466	8
β-strand	468-475	8	1
α-helix	480-491	12
β-strand	494-499	6	1
α-helix	500-501	2
β-strand	510-516	7	1
β-strand	521-527	7	1
α-helix	530-547	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mediator of RNA polymerase II transcription subunit 25	A	protein	159	HOMO SAPIENS	Q71SY5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2XNF_1 MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 25 (chains A)
MSVSNKLLAWSGVLEWQEKPKPASVDANTKLTRSLPCQVYVNHGENLKTEQWPQKLIMQL
IPQQLLTTLGPLFRNSRMVQFHFTNKDLESLKGLYRIMGNGFAGCVHFPHTAPCEVRVLM
LLYSSKKKIFMGLIPYDQSGFVNGIRQVITNLEHHHHHH

Primary citation

Structure and Vp16 Binding of the Mediator Med25 Activator Interaction Domain. Vojnic, E., Mourao, A., Seizl, M. et al. Nat Struct Mol Biol (2011) 18:404. DOI 10.1038/NSMB.1997 · PubMed

Other PDB entries of the same protein (UniProt Q71SY5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9CCV 2.53 Å, Crystal structure of human respiratory syncytial virus NS1 bound to human MED25 ACID
7EMF 3.5 Å, Human Mediator (deletion of MED1-IDR) in a Tail-extended conformation
8GXS 4.16 Å, PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state
8T9D 4.66 Å, CryoEM structure of TR-TRAP
7LBM 4.8 Å, Structure of the human Mediator-bound transcription pre-initiation complex
8GXQ 5.04 Å, PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state
2KY6 Structure of ARC92VBD/MED25ACID
2L23 NMR structure of the ACID (ACtivator Interacting Domain) of the human mediator Med25…
2L6U Solution NMR Structure of Med25(391-543) Comprising the Activator-Interacting Domain…

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