5U0P

Cryo-EM structure of the transcriptional Mediator


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mediator structure and rearrangements required for holoenzyme formation.

Tsai, K.L.Yu, X.Gopalan, S.Chao, T.C.Zhang, Y.Florens, L.Washburn, M.P.Murakami, K.Conaway, R.C.Conaway, J.W.Asturias, F.J.

(2017) Nature 544: 196-201

  • DOI: 10.1038/nature21393
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The conserved Mediator co-activator complex has an essential role in the regulation of RNA polymerase II transcription in all eukaryotes. Understanding the structure and interactions of Mediator is crucial for determining how the complex influences t ...

    The conserved Mediator co-activator complex has an essential role in the regulation of RNA polymerase II transcription in all eukaryotes. Understanding the structure and interactions of Mediator is crucial for determining how the complex influences transcription initiation and conveys regulatory information to the basal transcription machinery. Here we present a 4.4 Å resolution cryo-electron microscopy map of Schizosaccharomyces pombe Mediator in which conserved Mediator subunits are individually resolved. The essential Med14 subunit works as a central backbone that connects the Mediator head, middle and tail modules. Comparison with a 7.8 Å resolution cryo-electron microscopy map of a Mediator-RNA polymerase II holoenzyme reveals that changes in the structure of Med14 facilitate a large-scale Mediator rearrangement that is essential for holoenzyme formation. Our study suggests that access to different conformations and crosstalk between structural elements are essential for the Mediator regulation mechanism, and could explain the capacity of the complex to integrate multiple regulatory signals.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mediator complex subunit 14
N
931Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med14 (pmc1)
Find proteins for Q9P7Y4 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9P7Y4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mediator complex subunit 6
F
216Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med6 (pmc5)
Find proteins for Q9US45 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9US45
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Mediator complex subunit 8
H
200Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med8 (sep15)
Find proteins for O94646 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O94646
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Mediator complex subunit 17
Q
545Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med17 (srb4)
Find proteins for P87306 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P87306
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Mediator complex subunit 18
R
207Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med18 (pmc6, sep11)
Find proteins for O14198 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O14198
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Mediator complex subunit 20
T
193Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med20
Find proteins for Q10317 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q10317
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Mediator complex subunit 11
K
116Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med11
Find proteins for Q9P6Q0 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9P6Q0
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Mediator complex subunit 22
V
136Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med22 (srb6)
Find proteins for O14010 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O14010
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Mediator complex subunit 4
D
239N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Mediator complex subunit 7
G
376Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med7
Find proteins for O60104 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O60104
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Mediator complex subunit 21
U
138Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med21 (srb7)
Find proteins for O94376 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O94376
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Mediator complex subunit 31
3
139Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med31 (sep10)
Find proteins for Q9USH1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9USH1
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Mediator complex subunit 9
I
121Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Find proteins for O13964 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O13964
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Mediator complex subunit 27
2
273Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med27 (pmc3)
Find proteins for Q10477 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q10477
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Mediator complex subunit 19
S
139N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Mediator complex subunit 10
J
132N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
D, J, N, S
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-03-15
    Type: Database references
  • Version 1.2: 2017-04-19
    Type: Database references
  • Version 1.3: 2018-07-18
    Type: Data collection