5OQM

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.80 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

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

  • DOI: 10.1038/nature24282
  • Primary Citation of Related Structures:  
    5OQJ, 5OQM

  • PubMed Abstract: 
  • For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron microscopy structures of the Saccharomyces cerevisiae PIC and PIC-core Mediator complex at nominal resolutions of 4 ...

    For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron microscopy structures of the Saccharomyces cerevisiae PIC and PIC-core Mediator complex at nominal resolutions of 4.7 Å and 5.8 Å, respectively. The structures reveal transcription factor IIH (TFIIH), and suggest how the core and kinase TFIIH modules function in the opening of promoter DNA and the phosphorylation of Pol II, respectively. The TFIIH core subunit Ssl2 (a homologue of human XPB) is positioned on downstream DNA by the 'E-bridge' helix in TFIIE, consistent with TFIIE-stimulated DNA opening. The TFIIH kinase module subunit Tfb3 (MAT1 in human) anchors the kinase Kin28 (CDK7), which is mobile in the PIC but preferentially located between the Mediator hook and shoulder in the PIC-core Mediator complex. Open spaces between the Mediator head and middle modules may allow access of the kinase to its substrate, the C-terminal domain of Pol II.


    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
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1A1733Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO21RPB1RPB220SUA8YDL140CD2150
EC: 2.7.7.6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2B1224Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB2RPB150RPO22YOR151C
EC: 2.7.7.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3C318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB3YIL021W
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4D221Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB4YJL140WJ0654
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1E215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB5RPA7RPC9YBR154CYBR1204
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2F155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO26RPB6YPR187WP9677.8
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7G171Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB7YDR404CD9509.22
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3H146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB8YOR224CYOR50-14
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Entity ID: 9
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DNA-directed RNA polymerase II subunit RPB9I122Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB9YGL070C
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5J70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB10YOR210W
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11K120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB11YOL005C
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Entity ID: 12
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DNA-directed RNA polymerases I, II, and III subunit RPABC4L70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC10RPB12YHR143W-AYHR143BW
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIBM345Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUA7YPR086WP9513.4
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
TATA-box-binding proteinO240Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPT15BTF1TBP1YER148W
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIF subunit alphaP [auth Q]747Saccharomyces cerevisiae S288CSaccharomyces cerevisiaeMutation(s): 0 
Gene Names: TFG1SSU71YGR186WG7526SCKG_1591
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Entity ID: 17
MoleculeChainsSequence 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
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIA large subunitS [auth U]286Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOA1YOR194C
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2T [auth V]122Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOA2YKL058W
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor TFIIE subunitU [auth W]541Saccharomyces cerevisiaeSaccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFA1SCKG_3819YKL028W
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit betaV [auth X]328Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFA2YKR062W
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPDW [auth 0]778Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RAD3REM1YER171W
EC: 3.6.4.12
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit TFB1X [auth 1]510Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFB1YDR311WD9740.3
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit TFB2Y [auth 2]553Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFB2YPL122C
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II transcription factor B subunit 3Z [auth 3]321Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFB3RIG2YDR460W
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit TFB4AA [auth 4]333Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFB4YPR056W
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit TFB5BA [auth 5]72Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TFB5YDR079C-A
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit SSL1CA [auth 6]461Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SSL1YLR005W
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Find proteins for Q04673 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPBDA [auth 7]843Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SSL2LOM3RAD25UVS112YIL143C
EC: 3.6.4.12
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown proteinEA [auth Z]43Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6FA [auth a]295Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MED6MTR32YHR058C
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 8GA [auth b]223Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MED8YBR193CYBR1403
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11HA [auth c]115Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MED11YMR112CYM9718.11C
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Entity ID: 35
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Mediator of RNA polymerase II transcription subunit 17IA [auth d]687Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SRB4MED17YER022W
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18JA [auth e]307Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SRB5MED18YGR104C
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20KA [auth f]210Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SRB2HRS2MED20YHR041C
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22LA [auth g]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SRB6MED22YBR253WYBR1721
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 4MA [auth h]300Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MED4YOR174WO3630
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7NA [auth i]223Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MED7YOL135C
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 9OA [auth j]149Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSE2MED9YNR010WN2046
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 10PA [auth k]157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUT2MED10YPR168WP9325.2
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 14QA [auth l]745Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RGR1MED14YLR071C
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 19RA [auth m]220Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ROX3MED19NUT3SSN7YBL093CYBL0837
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 21SA [auth n]140Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SRB7MED21YDR308CD9740.17
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 31,Mediator of RNA polymerase II transcription subunit 31TA [auth o]151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SOH1MED31YGL127CG2864
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Entity ID: 14
MoleculeChainsLengthOrganismImage
NONTEMPLATE DNAN106synthetic construct
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Entity ID: 18
MoleculeChainsLengthOrganismImage
TEMPLATE DNAR [auth T]106synthetic construct
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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FB [auth 0]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

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AB [auth I] , BB [auth J] , CB [auth L] , DB [auth M] , EB [auth W] , GB [auth 3] , HB [auth 3] , IB [auth 4] , 
AB [auth I],  BB [auth J],  CB [auth L],  DB [auth M],  EB [auth W],  GB [auth 3],  HB [auth 3],  IB [auth 4],  JB [auth 6],  KB [auth 6],  LB [auth 6],  UA [auth A],  VA [auth A],  XA [auth B],  YA [auth C],  ZA [auth I]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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WA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.80 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
German Research FoundationGermanySPP1935
Volkswagen FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations