3RJ1

Architecture of the Mediator Head module


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.373 
  • R-Value Work: 0.345 
  • R-Value Observed: 0.348 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Architecture of the Mediator head module.

Imasaki, T.Calero, G.Cai, G.Tsai, K.L.Yamada, K.Cardelli, F.Erdjument-Bromage, H.Tempst, P.Berger, I.Kornberg, G.L.Asturias, F.J.Kornberg, R.D.Takagi, Y.

(2011) Nature 475: 240-243

  • DOI: 10.1038/nature10162
  • Primary Citation of Related Structures:  
    3RJ1

  • PubMed Abstract: 
  • Mediator is a key regulator of eukaryotic transcription, connecting activators and repressors bound to regulatory DNA elements with RNA polymerase II (Pol II). In the yeast Saccharomyces cerevisiae, Mediator comprises 25 subunits with a total mass of more than one megadalton (refs 5, 6) and is organized into three modules, called head, middle/arm and tail ...

    Mediator is a key regulator of eukaryotic transcription, connecting activators and repressors bound to regulatory DNA elements with RNA polymerase II (Pol II). In the yeast Saccharomyces cerevisiae, Mediator comprises 25 subunits with a total mass of more than one megadalton (refs 5, 6) and is organized into three modules, called head, middle/arm and tail. Our understanding of Mediator assembly and its role in regulating transcription has been impeded so far by limited structural information. Here we report the crystal structure of the essential Mediator head module (seven subunits, with a mass of 223 kilodaltons) at a resolution of 4.3 ångströms. Our structure reveals three distinct domains, with the integrity of the complex centred on a bundle of ten helices from five different head subunits. An intricate pattern of interactions within this helical bundle ensures the stable assembly of the head subunits and provides the binding sites for general transcription factors and Pol II. Our structural and functional data suggest that the head module juxtaposes transcription factor IIH and the carboxy-terminal domain of the largest subunit of Pol II, thereby facilitating phosphorylation of the carboxy-terminal domain of Pol II. Our results reveal architectural principles underlying the role of Mediator in the regulation of gene expression.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11A, H, O131Saccharomyces cerevisiaeMutation(s): 2 
Gene Names: MED11YMR112CYM9718.11C
UniProt
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UniProt GroupQ99278
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17B, I, P583Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SRB4MED17YER022W
UniProt
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UniProt GroupP32569
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 8C, J, Q223Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MED8YBR193CYBR1403
UniProt
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UniProt GroupP38304
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22D, K, R121Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SRB6MED22YBR253WYBR1721
UniProt
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UniProt GroupP32570
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18E, L, S275Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SRB5MED18YGR104C
UniProt
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UniProt GroupP32585
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20F, M, T210Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SRB2HRS2MED20YHR041C
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6G, N, U295Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MED6MTR32YHR058C
UniProt
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SE
Query on SE

Download Ideal Coordinates CCD File 
AA [auth B],
AB [auth H],
AC [auth L],
AD [auth R],
BA [auth B],
AA [auth B],
AB [auth H],
AC [auth L],
AD [auth R],
BA [auth B],
BB [auth H],
BC [auth M],
BD [auth S],
CA [auth B],
CB [auth I],
CC [auth M],
CD [auth S],
DA [auth B],
DB [auth I],
DC [auth M],
DD [auth S],
EA [auth B],
EB [auth I],
EC [auth N],
ED [auth S],
FA [auth B],
FB [auth I],
FC [auth N],
FD [auth S],
GA [auth B],
GB [auth I],
GC [auth N],
GD [auth S],
HA [auth C],
HB [auth I],
HC [auth N],
HD [auth T],
IA [auth C],
IB [auth I],
IC [auth N],
ID [auth T],
JA [auth C],
JB [auth I],
JC [auth O],
JD [auth U],
KA [auth C],
KB [auth I],
KC [auth O],
KD [auth U],
LA [auth D],
LB [auth I],
LC [auth O],
LD [auth U],
MA [auth D],
MB [auth J],
MC [auth P],
MD [auth U],
NA [auth D],
NB [auth J],
NC [auth P],
ND [auth U],
OA [auth E],
OB [auth J],
OC [auth P],
OD [auth U],
PA [auth E],
PB [auth J],
PC [auth P],
QA [auth E],
QB [auth K],
QC [auth P],
RA [auth E],
RB [auth K],
RC [auth P],
SA [auth E],
SB [auth K],
SC [auth P],
TA [auth E],
TB [auth K],
TC [auth P],
UA [auth G],
UB [auth L],
UC [auth P],
V [auth A],
VA [auth G],
VB [auth L],
VC [auth Q],
W [auth A],
WA [auth G],
WB [auth L],
WC [auth Q],
X [auth A],
XA [auth G],
XB [auth L],
XC [auth Q],
Y [auth B],
YA [auth G],
YB [auth L],
YC [auth Q],
Z [auth B],
ZA [auth H],
ZB [auth L],
ZC [auth R]
SELENIUM ATOM
Se
SPVXKVOXSXTJOY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, H, O L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.373 
  • R-Value Work: 0.345 
  • R-Value Observed: 0.348 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 265.914α = 90
b = 265.914β = 90
c = 319.948γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-27
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Advisory, Refinement description, Source and taxonomy