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 1.2 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 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 Diseases (NIH/NIAID)United StatesAI21144
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM49985
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM36659
National Science Foundation (NSF, United States)United States1231306
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103481

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence
  • Version 1.2: 2019-11-27
    Type: Author supporting evidence