3RJ1 | pdb_00003rj1

Architecture of the Mediator Head module

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 
    0.373 (Depositor), 0.340 (DCC) 
  • R-Value Work: 
    0.345 (Depositor), 0.341 (DCC) 
  • R-Value Observed: 
    0.348 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 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: https://doi.org/10.1038/nature10162
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 636.19 kDa 
  • Atom Count: 17,945 
  • Modeled Residue Count: 3,594 
  • Deposited Residue Count: 5,514 
  • Unique protein chains: 7

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11
A, H, O
131Saccharomyces cerevisiaeMutation(s): 2 
Gene Names: MED11, YMR112C, YM9718.11C
UniProt
Find proteins for Q99278 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ99278
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17
B, I, P
583Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SRB4, MED17, YER022W
UniProt
Find proteins for P32569 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 8
C, J, Q
223Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MED8, YBR193C, YBR1403
UniProt
Find proteins for P38304 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22
D, K, R
121Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SRB6, MED22, YBR253W, YBR1721
UniProt
Find proteins for P32570 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18
E, L, S
275Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SRB5, MED18, YGR104C
UniProt
Find proteins for P32585 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20
F, M, T
210Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SRB2, HRS2, MED20, YHR041C
UniProt
Find proteins for P34162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6
G, N, U
295Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MED6, MTR32, YHR058C
UniProt
Find proteins for P38782 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / 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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, H, O
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
UNK
Query on UNK
B, I, P
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free:  0.373 (Depositor), 0.340 (DCC) 
  • R-Value Work:  0.345 (Depositor), 0.341 (DCC) 
  • R-Value Observed: 0.348 (Depositor) 
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 

Deposition Data

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
  • Version 1.2: 2024-11-06
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary