1YKE: Mediator MED7/MED21 subcomplex

Structure of the mediator MED7/MED21 subcomplex. Determined by X-ray diffraction at 3.3 Å resolution. Released 22 Feb 2005.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 3,548
Mol. weight: 60.68 kDa
Released: 22 Feb 2005

Explore 1YKE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YKE contains 14 α-helices and 0 β-strands across 4 chains. 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: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	112-134	23
α-helix	141-164	24
α-helix	166-203	38

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	5-18	14
α-helix	23-28	6
α-helix	31-34	4
α-helix	52-79	28
α-helix	87-127	41

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	112-132	21
α-helix	144-161	18
α-helix	166-202	37

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	5-25	21
α-helix	56-79	24
α-helix	87-128	42

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA polymerase II mediator complex protein MED7	A, C	protein	108	Saccharomyces cerevisiae	Q08278 (AlphaFold model)
RNA polymerase II holoenzyme component SRB7	B, D	protein	151	Saccharomyces cerevisiae	P47822 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1YKE_1 RNA polymerase II mediator complex protein MED7 (chains A, C)
MASMKKSTENESTNYQYKIQELRKLLKSLLLNYLELIGVLSINPDMYERKVENIRTILVN
IHHLLNEYRPHQSRESLIMLLEEQLEYKRGEIREIEQVCKQVHDKLTS

Sequence of entity 2 (B, D), FASTA

>1YKE_2 RNA polymerase II holoenzyme component SRB7 (chains B, D)
MTDRLTQLQICLDQMTEQFCATLNYIDKNHGFERLTVNEPQMSDKHATVVPPEEFSNTID
ELSTDIILKTRQINKLIDSLPGVDVSAEEQLRKIDMLQKKLVEVEDEKIEAIKKKEKLLR
HVDSLIEDFVDGIANSKKSTAAALEHHHHHH

Primary citation

A conserved mediator hinge revealed in the structure of the MED7.MED21 (Med7.Srb7) heterodimer. Baumli, S., Hoeppner, S., Cramer, P. J Biol Chem (2005) 280:18171-18178. DOI 10.1074/jbc.M413466200 · PubMed

Other PDB entries of the same protein (UniProt Q08278 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FBI 2.8 Å, Structure of the Mediator submodule Med7N/31
1YKH 3.0 Å, Structure of the mediator MED7/MED21 (Med7/Srb7) subcomplex
8CEN 3.0 Å, Yeast RNA polymerase II transcription pre-initiation complex with core Mediator
3FBN 3.01 Å, Structure of the Mediator submodule Med7N/31
7UI9 3.3 Å, Core Mediator-PICearly (Copy A)
7UIO 3.3 Å, Mediator-PIC Early (Composite Model)
9PC8 3.4 Å, Core Mediator of PIC-Med-SWI/SNF
8CEO 3.6 Å, Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the…
7UIG 4.3 Å, Mediator-PIC Early (Mediator A)
7UIF 4.6 Å, Mediator-PIC Early (Core B)
5OQM 5.8 Å, Structure of yeast transcription pre-initiation complex with tfiih and core mediator
5SVA 15.3 Å, Mediator-RNA Polymerase II Pre-Initiation Complex

Browse structure collections

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