5SVA

Mediator-RNA Polymerase II Pre-Initiation Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 15.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex.

Robinson, P.J.Trnka, M.J.Bushnell, D.A.Davis, R.E.Mattei, P.J.Burlingame, A.L.Kornberg, R.D.

(2016) Cell 166: 1411-1422.e16

  • DOI: 10.1016/j.cell.2016.08.050

  • PubMed Abstract: 
  • A complete, 52-protein, 2.5 million dalton, Mediator-RNA polymerase II pre-initiation complex (Med-PIC) was assembled and analyzed by cryo-electron microscopy and by chemical cross-linking and mass spectrometry. The resulting complete Med-PIC structu ...

    A complete, 52-protein, 2.5 million dalton, Mediator-RNA polymerase II pre-initiation complex (Med-PIC) was assembled and analyzed by cryo-electron microscopy and by chemical cross-linking and mass spectrometry. The resulting complete Med-PIC structure reveals two components of functional significance, absent from previous structures, a protein kinase complex and the Mediator-activator interaction region. It thereby shows how the kinase and its target, the C-terminal domain of the polymerase, control Med-PIC interaction and transcription.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: kornberg@stanford.edu.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB1
A
1733Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPO21 (RPB1, RPB220, SUA8)
EC: 2.7.7.6
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04050
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB2
B
1224Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB2 (RPB150, RPO22)
EC: 2.7.7.6
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P08518
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB3
C
318Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB3
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P16370
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB4
D
221Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB4
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20433
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC1
E
215Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB5 (RPA7, RPC9)
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20434
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC2
F
155Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPO26 (RPB6)
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20435
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB7
G
171Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB7
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P34087
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3
H
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB8
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20436
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB9
I
122Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB9
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P27999
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5
J
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB10
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22139
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB11
K
120Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB11
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38902
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4
L
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC10 (RPB12)
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40422
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 6
M
295Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MED6 (MTR32)
Find proteins for P38782 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MED6
Go to UniProtKB:  P38782
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 8
N
223Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MED8
Find proteins for P38304 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MED8
Go to UniProtKB:  P38304
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 11
O
115Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MED11
Find proteins for Q99278 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MED11
Go to UniProtKB:  Q99278
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 17
P
687Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SRB4 (MED17)
Find proteins for P32569 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32569
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 18
Q
307Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SRB5 (MED18)
Find proteins for P32585 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32585
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 20
R
210Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SRB2 (HRS2, MED20)
Find proteins for P34162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P34162
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 22
S
121Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SRB6 (MED22)
Find proteins for P32570 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32570
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 4
T
284Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MED4
Find proteins for Q12343 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MED4
Go to UniProtKB:  Q12343
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 7
U
222Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MED7
Find proteins for Q08278 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MED7
Go to UniProtKB:  Q08278
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 9
V
149Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CSE2 (MED9)
Find proteins for P33308 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33308
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 21
W
140Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SRB7 (MED21)
Find proteins for P47822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P47822
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 31
X
127Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SOH1 (MED31)
Find proteins for P38633 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38633
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
DNA repair helicase RAD3
Y
778Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RAD3 (REM1)
EC: 3.6.4.12
Find proteins for P06839 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P06839
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
DNA repair helicase RAD25
Z
843Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SSL2 (LOM3, RAD25, UVS112)
EC: 3.6.4.12
Find proteins for Q00578 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q00578
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II transcription factor B subunit 2
a
513Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TFB2
Find proteins for Q02939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02939
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II transcription factor B subunit 5
b
72Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TFB5
Find proteins for Q3E7C1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E7C1
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIB
c
345Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SUA7
Find proteins for P29055 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P29055
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIA large subunit
d
286Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TOA1
Find proteins for P32773 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32773
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIA subunit 2
e
122Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TOA2
Find proteins for P32774 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32774
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIF subunit alpha
f
735Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TFG1 (SSU71)
Find proteins for P41895 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41895
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIF subunit beta
g
400Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TFG2
Find proteins for P41896 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41896
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIE subunit alpha
h
482Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TFA1
Find proteins for P36100 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36100
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIE subunit beta
i
328Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TFA2
Find proteins for P36145 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36145
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
TATA-box-binding protein
j
240Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SPT15 (BTF1, TBP1)
Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P13393
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB1
k
25Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPO21 (RPB1, RPB220, SUA8)
EC: 2.7.7.6
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04050
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor TFIID subunit 14
n
244Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TAF14 (ANC1, CST10, SWP29, TAF30, TFG3)
Find proteins for P35189 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P35189
Entity ID: 38
MoleculeChainsLengthOrganism
108bp HIS4 Promoter Non-template Strand (-92/+16)l108Saccharomyces cerevisiae
Entity ID: 39
MoleculeChainsLengthOrganism
108bp HIS4 Promoter Template Strand (+16/-92)m108Saccharomyces cerevisiae
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, I, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 15.3 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 Allergy and Infectious DiseasesUnited StatesAI21144
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM49985
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM36659
National Science Foundation (United States)United States1231306
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM103481

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence