5U0S

Cryo-EM structure of the Mediator-RNAPII complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 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 Biochemistry &Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA.,Stowers Institute for Medical Research, Kansas City, Missouri, USA.,Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego School of Medicine, La Jolla, California, USA.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City Kansas, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA.,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 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: 2
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: 3
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: 4
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: 5
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: 6
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: 7
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: 8
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: 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 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: 14
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: 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.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit Rpb1
a
1752Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb1
EC: 2.7.7.6
Find proteins for P36594 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P36594
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit Rpb2
b
1210Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb2
EC: 2.7.7.6
Find proteins for Q02061 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q02061
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit Rpb3
c
297Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb3
Find proteins for P37382 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P37382
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit Rpb4
d
135Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb4
Find proteins for O74825 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O74825
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit Rpb5
e
210Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb5
Find proteins for Q09191 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q09191
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit Rpb6
f
142Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb6 (rpo15)
Find proteins for P36595 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P36595
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit Rpb7
g
172Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb7
Find proteins for O14459 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O14459
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit Rpb8
h
125Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb8
Find proteins for Q92399 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q92399
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit Rpb9
i
113Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb9
Find proteins for O74635 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O74635
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit Rpb10
j
71Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb10
Find proteins for O13877 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O13877
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit Rpb11
k
123Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpb11
Find proteins for P87123 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P87123
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit Rpb12
l
63Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpc10 (rpb12)
Find proteins for P48011 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P48011
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: 7.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM67167
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM41628

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: 2017-09-13
    Type: Author supporting evidence, Data collection
  • Version 1.4: 2018-07-18
    Type: Data collection, Experimental preparation