6GYK

Structure of a yeast closed complex (core CC1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.10 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

Promoter Distortion and Opening in the RNA Polymerase II Cleft.

Dienemann, C.Schwalb, B.Schilbach, S.Cramer, P.

(2019) Mol Cell 73: 97-106.e4

  • DOI: https://doi.org/10.1016/j.molcel.2018.10.014
  • Primary Citation of Related Structures:  
    6GYK, 6GYL, 6GYM

  • PubMed Abstract: 

    Transcription initiation requires opening of promoter DNA in the RNA polymerase II (Pol II) pre-initiation complex (PIC), but it remains unclear how this is achieved. Here we report the cryo-electron microscopic (cryo-EM) structure of a yeast PIC that contains underwound, distorted promoter DNA in the closed Pol II cleft. The DNA duplex axis is offset at the upstream edge of the initially melted DNA region (IMR) where DNA opening begins. Unstable IMRs are found in a subset of yeast promoters that we show can still initiate transcription after depletion of the transcription factor (TF) IIH (TFIIH) translocase Ssl2 (XPB in human) from the nucleus in vivo. PIC-induced DNA distortions may thus prime the IMR for melting and may explain how unstable IMRs that are predicted in promoters of Pol I and Pol III can open spontaneously. These results suggest that DNA distortion in the polymerase cleft is a general mechanism that contributes to promoter opening.


  • Organizational Affiliation

    Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11,733Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB21,224Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3318Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4220Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1215Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2154Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7171Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3146Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9122Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC570Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11120Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC470Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIB345Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUA7YPR086WP9513.4
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-box-binding protein240Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPT15BTF1TBP1YER148W
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIF subunit alphaP [auth Q]735Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFG1SSU71YGR186WG7526
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIF subunit betaQ [auth R]400Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFG2YGR005C
EC: 3.6.4.12
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA large subunit,Transcription initiation factor IIA large subunitS [auth U]171Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOA1YOR194C
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2T [auth V]129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOA2YKL058W
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Entity ID: 14
MoleculeChains LengthOrganismImage
GAT1 Promoter56Saccharomyces cerevisiae S288C
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Entity ID: 18
MoleculeChains LengthOrganismImage
GAT1 promoter DNAR [auth T]56Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth I]
BA [auth J]
CA [auth L]
DA [auth M]
U [auth A]
AA [auth I],
BA [auth J],
CA [auth L],
DA [auth M],
U [auth A],
V [auth A],
X [auth B],
Y [auth C],
Z [auth I]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
W [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilGermany693023
German Research FoundationGermanySFB860

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Advisory, Data collection, Database references, Derived calculations
  • Version 1.2: 2019-12-18
    Changes: Other