5OQM

STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structures of transcription pre-initiation complex with TFIIH and Mediator.

Schilbach, S.Hantsche, M.Tegunov, D.Dienemann, C.Wigge, C.Urlaub, H.Cramer, P.

(2017) Nature 551: 204-209


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
Transcription initiation factor IIB
M
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: 15
MoleculeChainsSequence LengthOrganismDetails
TATA-box-binding protein
O
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: 16
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIF subunit alpha
Q
747N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIF subunit beta
R
400Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TFG2
EC: 3.6.4.12
Find proteins for P41896 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41896
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIA large subunit
U
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: 20
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIA subunit 2
V
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: 21
MoleculeChainsSequence LengthOrganismDetails
Transcription factor TFIIE subunit
W
541N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIE subunit beta
X
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: 23
MoleculeChainsSequence LengthOrganismDetails
General transcription and DNA repair factor IIH helicase subunit XPD
0
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: 24
MoleculeChainsSequence LengthOrganismDetails
General transcription and DNA repair factor IIH subunit TFB1
1
510Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TFB1
Find proteins for P32776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32776
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
General transcription and DNA repair factor IIH subunit TFB2
2
553Saccharomyces 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: 26
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II transcription factor B subunit 3
3
321Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TFB3 (RIG2)
Find proteins for Q03290 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03290
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
General transcription and DNA repair factor IIH subunit TFB4
4
333Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TFB4
Find proteins for Q12004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12004
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
General transcription and DNA repair factor IIH subunit TFB5
5
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
General transcription and DNA repair factor IIH subunit SSL1
6
461Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SSL1
Find proteins for Q04673 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q04673
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
General transcription and DNA repair factor IIH helicase subunit XPB
7
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: 31
MoleculeChainsSequence LengthOrganismDetails
Unknown protein
Z
43N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 6
a
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: 33
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 8
b
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: 34
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 11
c
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: 35
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 17
d
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: 36
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 18
e
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: 37
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 20
f
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: 38
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 22
g
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: 39
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 4
h
300Saccharomyces 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: 40
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 7
i
223Saccharomyces 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: 41
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 9
j
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: 42
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 10
k
157Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NUT2 (MED10)
Find proteins for Q06213 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06213
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 14
l
745Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RGR1 (MED14)
Find proteins for P19263 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P19263
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 19
m
220Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ROX3 (MED19, NUT3, SSN7)
Find proteins for P25046 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25046
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 21
n
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: 46
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 31,Mediator of RNA polymerase II transcription subunit 31
o
151Saccharomyces 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: 14
MoleculeChainsLengthOrganism
NONTEMPLATE DNAN106synthetic construct
Entity ID: 18
MoleculeChainsLengthOrganism
TEMPLATE DNAT106synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
0
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
3, 4, 6, A, B, C, I, J, L, M, W
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
0, 1, 2, 4, 6, 7, h, o, Q, W, Z
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.8 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
European Research CouncilGermany693023
German Research FoundationGermanySFB860
German Research FoundationGermanySPP1935
Volkswagen FoundationGermany--

Revision History 

  • Version 1.0: 2018-05-09
    Type: Initial release