7ML3

General transcription factor TFIIH (weak binding)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.60 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: https://doi.org/10.1016/j.molcel.2021.12.020
  • Primary Citation of Related Structures:  
    7MEI, 7MK9, 7MKA, 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. 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BJ4_G0050160.mRNA.1.CDS.1A [auth 3]321Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q03290 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II transcription factor B subunit 2B [auth 2]513Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPDC [auth 0]778Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12 (PDB Primary Data), 5.6.2.3 (UniProt)
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Tfb1D [auth 1]537Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit TFB4E [auth 4]338Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIHF [auth 6]461Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit TFB5G [auth 5]72Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPBH [auth 7]843Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt
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Entity ID: 9
MoleculeChains LengthOrganismImage
non-template strand DNAI [auth N]30Saccharomyces cerevisiae
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Entity ID: 10
MoleculeChains LengthOrganismImage
template strand DNAJ [auth T]30Saccharomyces cerevisiae
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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M [auth 0]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN

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K [auth 3]
L [auth 3]
N [auth 4]
O [auth 6]
P [auth 6]
K [auth 3],
L [auth 3],
N [auth 4],
O [auth 6],
P [auth 6],
Q [auth 6],
R [auth 6]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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