7ML0

RNA polymerase II pre-initiation complex (PIC1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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

Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.

Yang, C.Fujiwara, R.Kim, H.J.Basnet, P.Zhu, Y.Gorbea Colon, J.J.Steimle, S.Garcia, B.A.Kaplan, C.D.Murakami, K.

(2022) Mol Cell 82: 660-676.e9

  • DOI: 10.1016/j.molcel.2021.12.020
  • Primary Citation of Related Structures:  
    7MEI, 7ML0, 7ML1, 7ML2, 7ML3, 7ML4

  • PubMed Abstract: 
  • Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we report multiple structures of initiation complexes converted de novo from a 33-subunit yeast pre-initiation complex (PIC) through catalytic activities and subsequently stalled at different template positions ...

    Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we report multiple structures of initiation complexes converted de novo from a 33-subunit yeast pre-initiation complex (PIC) through catalytic activities and subsequently stalled at different template positions. We determine that PICs in the initially transcribing complex (ITC) can synthesize a transcript of ∼26 nucleotides before transitioning to an elongation complex (EC) as determined by the loss of general transcription factors (GTFs). Unexpectedly, transition to an EC was greatly accelerated when an ITC encountered a downstream EC stalled at promoter proximal regions and resulted in a collided head-to-end dimeric EC complex. Our structural analysis reveals a dynamic state of TFIIH, the largest of GTFs, in PIC/ITC with distinct functional consequences at multiple steps on the pathway to elongation.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: kenjim@pennmedicine.upenn.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunitA1,733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaB1,224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3C318Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4D221Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1E215Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
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DNA-directed RNA polymerases I,II,and III subunit RPABC2F155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7G171Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
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DNA-directed RNA polymerases I, II, and III subunit RPABC3H146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
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DNA-directed RNA polymerase II subunit RPB9I122Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
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DNA-directed RNA polymerases II subunit RPABC5J70Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
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DNA-directed RNA polymerase II subunit RPB11K120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
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DNA-directed RNA polymerases II subunit RPABC4L70Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIBM345Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIF subunit alphaN [auth Q]735Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIF subunit betaO [auth R]400Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit alphaP [auth W]482Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
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Transcription initiation factor IIE subunit betaQ [auth X]328Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
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TATA-box-binding proteinR [auth O]240Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPDU [auth 0]778Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 22
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DNA-directed RNA polymerase subunitV [auth 1]541Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4W [auth 4]338Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit SSL1X [auth 6]461Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II transcription factor B subunit 2Y [auth 2]513Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit TFB5Z [auth 5]72Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
BJ4_G0050160.mRNA.1.CDS.1AA [auth 3]321Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPBBA [auth 7]843Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 19
MoleculeChainsLengthOrganismImage
template strand DNAS [auth T]66Saccharomyces cerevisiae
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Entity ID: 20
MoleculeChainsLengthOrganismImage
non-template strand DNAT [auth N]66Saccharomyces cerevisiae
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM123233
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA196539
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesAG031862
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24GM129547
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10OD023592

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references