6GYL

Structure of a yeast closed complex with distorted DNA (core CCdist)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 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 ...

    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. Electronic address: patrick.cramer@mpibpc.mpg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11,733Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO21, RPB1, RPB220, SUA8, YDL140C, D2150
EC: 2.7.7.6
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Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB21,224Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB2, RPB150, RPO22, YOR151C
EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB3, YIL021W
UniProt
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4221Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB4, YJL140W, J0654
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB5, RPA7, RPC9, YBR154C, YBR1204
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO26, RPB6, YPR187W, P9677.8
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Entity ID: 7
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DNA-directed RNA polymerase II subunit RPB7171Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB7, YDR404C, D9509.22
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB8, YOR224C, YOR50-14
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Entity ID: 9
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DNA-directed RNA polymerase II subunit RPB9122Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB9, YGL070C
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Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
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DNA-directed RNA polymerases I, II, and III subunit RPABC570Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB10, YOR210W
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Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB11, YOL005C
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Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
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DNA-directed RNA polymerases I, II, and III subunit RPABC470Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC10, RPB12, YHR143W-A, YHR143BW
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Entity ID: 13
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Transcription initiation factor IIB345Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUA7, YPR086W, P9513.4
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
TATA-box-binding protein240Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPT15, BTF1, TBP1, YER148W
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIF subunit alphaP [auth Q]735Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFG1, SSU71, YGR186W, G7526
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Entity ID: 17
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Transcription initiation factor IIF subunit betaQ [auth R]400Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFG2, YGR005C
EC: 3.6.4.12
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIA large subunit,Transcription initiation factor IIA large subunitS [auth U]171Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOA1, YOR194C
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Find proteins for P32773 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
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Transcription initiation factor IIA subunit 2T [auth V]129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOA2, YKL058W
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit alpha,Tfa1,Tfa1U [auth W]586Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFA1, YKL028W
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Find proteins for P36100 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit betaV [auth X]328Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFA2, YKR062W
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Find proteins for P36145 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsLengthOrganismImage
GAT1 promoter DNA56Saccharomyces cerevisiae S288C
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Entity ID: 18
MoleculeChainsLengthOrganismImage
GAT1 promoter DNAR [auth T]56Saccharomyces cerevisiae S288C
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data
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: Data collection, Database references
  • Version 1.2: 2019-12-11
    Changes: Other