7O4K

Yeast TFIIH in the contracted state within the pre-initiation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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 RNA polymerase II pre-initiation complex at 2.9 angstrom defines initial DNA opening.

Schilbach, S.Aibara, S.Dienemann, C.Grabbe, F.Cramer, P.

(2021) Cell 

  • DOI: 10.1016/j.cell.2021.05.012
  • Primary Citation of Related Structures:  
    7O4L, 7O4J, 7O4K, 7O4I, 7O72, 7O75, 7O73

  • PubMed Abstract: 
  • Transcription initiation requires assembly of the RNA polymerase II (Pol II) pre-initiation complex (PIC) and opening of promoter DNA. Here, we present the long-sought high-resolution structure of the yeast PIC and define the mechanism of initial DNA opening ...

    Transcription initiation requires assembly of the RNA polymerase II (Pol II) pre-initiation complex (PIC) and opening of promoter DNA. Here, we present the long-sought high-resolution structure of the yeast PIC and define the mechanism of initial DNA opening. We trap the PIC in an intermediate state that contains half a turn of open DNA located 30-35 base pairs downstream of the TATA box. The initially opened DNA region is flanked and stabilized by the polymerase "clamp head loop" and the TFIIF "charged region" that both contribute to promoter-initiated transcription. TFIIE facilitates initiation by buttressing the clamp head loop and by regulating the TFIIH translocase. The initial DNA bubble is then extended in the upstream direction, leading to the open promoter complex and enabling start-site scanning and RNA synthesis. This unique mechanism of DNA opening may permit more intricate regulation than in the Pol I and Pol III systems.


    Organizational Affiliation

    Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. Electronic address: patrick.cramer@mpibpc.mpg.de.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPDA [auth 0]778Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RAD3REM1YER171W
EC: 3.6.4.12
UniProt
Find proteins for P06839 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06839 
Go to UniProtKB:  P06839
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit TFB1B [auth 1]645Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFB1YDR311WD9740.3
UniProt
Find proteins for P32776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32776 
Go to UniProtKB:  P32776
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit TFB2C [auth 2]517Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFB2YPL122C
UniProt
Find proteins for Q02939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02939 
Go to UniProtKB:  Q02939
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II transcription factor B subunit 3D [auth 3]324Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFB3RIG2YDR460W
UniProt
Find proteins for Q03290 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03290 
Go to UniProtKB:  Q03290
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit TFB4E [auth 4]341Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFB4YPR056W
UniProt
Find proteins for Q12004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12004 
Go to UniProtKB:  Q12004
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit TFB5F [auth 5]76Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFB5YDR079C-A
UniProt
Find proteins for Q3E7C1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q3E7C1 
Go to UniProtKB:  Q3E7C1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit SSL1G [auth 6]464Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SSL1YLR005W
UniProt
Find proteins for Q04673 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04673 
Go to UniProtKB:  Q04673
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPBH [auth 7]843Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SSL2LOM3RAD25UVS112YIL143C
EC: 3.6.4.12
UniProt
Find proteins for Q00578 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q00578 
Go to UniProtKB:  Q00578
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1I [auth A]1733Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO21RPB1RPB220SUA8YDL140CD2150
EC: 2.7.7.6
UniProt
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04050 
Go to UniProtKB:  P04050
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2J [auth B]1224Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB2RPB150RPO22YOR151C
EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P08518 
Go to UniProtKB:  P08518
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4K [auth D]221Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB4YJL140WJ0654
UniProt
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20433 
Go to UniProtKB:  P20433
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2L [auth F]155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO26RPB6YPR187WP9677.8
UniProt
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20435 
Go to UniProtKB:  P20435
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7M [auth G]177Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB7YDR404CD9509.22
UniProt
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P34087 
Go to UniProtKB:  P34087
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit alphaP [auth W]492Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFA1YKL028W
UniProt
Find proteins for P36100 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36100 
Go to UniProtKB:  P36100
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit betaQ [auth X]328Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFA2YKR062W
UniProt
Find proteins for P36145 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36145 
Go to UniProtKB:  P36145
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsLengthOrganismImage
Non-template DNAN106synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsLengthOrganismImage
Template DNAO [auth T]106synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
BA [auth 7]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
R [auth 0]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
BEF
Query on BEF

Download Ideal Coordinates CCD File 
Z [auth 7]BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth A] , DA [auth B] , EA [auth W] , S [auth 3] , T [auth 3] , U [auth 4] , V [auth 6] , W [auth 6] , 
CA [auth A],  DA [auth B],  EA [auth W],  S [auth 3],  T [auth 3],  U [auth 4],  V [auth 6],  W [auth 6],  X [auth 6],  Y [auth 6]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth 7]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionGermany894862
German Research Foundation (DFG)GermanyEXC 2067/1 39072994
German Research Foundation (DFG)GermanySFB860
German Research Foundation (DFG)GermanySPP2191
European Research Council (ERC)Germany882357

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Database references