6GYM

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.70 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
General transcription and DNA repair factor IIH helicase subunit XPD,General transcription and DNA repair factor IIH helicase subunit XPD,DNA repair helicase RAD3,DNA repair helicase RAD3,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
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UniProt GroupP06839
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit TFB1,General transcription and DNA repair factor IIH subunit TFB1,RNA polymerase II transcription factor B subunit 1,General transcription and DNA repair factor IIH subunit TFB1,RNA polymerase II transcription factor B subunit 1,General transcription and DNA repair factor IIH subunit TFB1,General transcription and DNA repair factor IIH subunit TFB1,General transcription and DNA repair factor IIH subunit TFB1,RNA polymerase II transcription factor B subunit 1,General transcription and DNA repair factor IIH subunit TFB1,RNA polymerase II transcription factor B subunit 1,General transcription and DNA repair factor IIH subunit TFB1,General transcription and DNA repair factor IIH subunit TFB1B [auth 1]641Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFB1YDR311WD9740.3
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2C [auth 2]462Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFB2YPL122C
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II transcription factor B subunit 3D [auth 3]321Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFB3RIG2YDR460W
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit TFB4,General transcription and DNA repair factor IIH subunit TFB4,RNA polymerase II transcription factor B subunit 4,General transcription and DNA repair factor IIH subunit TFB4,General transcription and DNA repair factor IIH subunit TFB4E [auth 4]338Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFB4YPR056W
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit TFB5F [auth 5]72Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFB5YDR079C-A
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1G [auth 6]461Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SSL1YLR005W
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPB,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,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
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1I [auth A]1,733Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2J [auth B]1,224Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3K [auth C]318Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4L [auth D]221Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1M [auth E]215Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2N [auth F]155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO26RPB6YPR187WP9677.8
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7O [auth G]171Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3P [auth H]146Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9Q [auth I]122Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5R [auth J]70Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11S [auth K]120Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4T [auth L]70Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIBU [auth M]345Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUA7YPR086WP9513.4
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-box-binding proteinV [auth O]240Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPT15BTF1TBP1YER148W
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIF subunit alphaW [auth Q]735Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFG1SSU71YGR186WG7526
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIF subunit betaX [auth R]400Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFG2YGR005C
EC: 3.6.4.12
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA large subunit,Transcription initiation factor IIA large subunitY [auth U]171Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOA1YOR194C
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2Z [auth V]122Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOA2YKL058W
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit alpha,Transcription initiation factor IIE subunit alpha,Transcription initiation factor IIE subunit alpha,Transcription initiation factor IIE subunit alpha,Transcription initiation factor IIE subunit alphaAA [auth W]332Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFA1YKL028W
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit betaBA [auth X]328Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFA2YKR062W
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown proteinCA [auth Z]43Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 30
MoleculeChains LengthOrganismImage
non-template DNA (HIS4)DA [auth N]75Saccharomyces cerevisiae S288C
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Entity ID: 31
MoleculeChains LengthOrganismImage
Template DNA (HIS4)EA [auth T]75Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
FA [auth 0]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN

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GA [auth 3]
HA [auth 3]
IA [auth 4]
JA [auth 6]
KA [auth 6]
GA [auth 3],
HA [auth 3],
IA [auth 4],
JA [auth 6],
KA [auth 6],
LA [auth 6],
MA [auth A],
NA [auth A],
PA [auth B],
QA [auth C],
RA [auth I],
SA [auth I],
TA [auth J],
UA [auth L],
VA [auth M],
WA [auth W]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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OA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A [auth 0]L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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: 2019-12-25
    Changes: Advisory, Derived calculations