8Q63

Cryo-EM structure of IC8', a second state of yeast mitochondrial RNA polymerase transcription initiation complex with 8-mer RNA, pppGpGpUpApApApUpG


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures illustrate step-by-step mitochondrial transcription initiation.

Goovaerts, Q.Shen, J.De Wijngaert, B.Basu, U.Patel, S.S.Das, K.

(2023) Nature 622: 872-879

  • DOI: https://doi.org/10.1038/s41586-023-06643-y
  • Primary Citation of Related Structures:  
    8AP1, 8ATT, 8ATV, 8ATW, 8C5S, 8C5U, 8Q63

  • PubMed Abstract: 

    Transcription initiation is a key regulatory step in gene expression during which RNA polymerase (RNAP) initiates RNA synthesis de novo, and the synthesized RNA at a specific length triggers the transition to the elongation phase. Mitochondria recruit a single-subunit RNAP and one or two auxiliary factors to initiate transcription. Previous studies have revealed the molecular architectures of yeast 1 and human 2 mitochondrial RNAP initiation complexes (ICs). Here we provide a comprehensive, stepwise mechanism of transcription initiation by solving high-resolution cryogenic electron microscopy (cryo-EM) structures of yeast mitochondrial RNAP and the transcription factor Mtf1 catalysing two- to eight-nucleotide RNA synthesis at single-nucleotide addition steps. The growing RNA-DNA is accommodated in the polymerase cleft by template scrunching and non-template reorganization, creating stressed intermediates. During early initiation, non-template strand scrunching and unscrunching destabilize the short two- and three-nucleotide RNAs, triggering abortive synthesis. Subsequently, the non-template reorganizes into a base-stacked staircase-like structure supporting processive five- to eight-nucleotide RNA synthesis. The expanded non-template staircase and highly scrunched template in IC8 destabilize the promoter interactions with Mtf1 to facilitate initiation bubble collapse and promoter escape for the transition from initiation to the elongation complex (EC). The series of transcription initiation steps, each guided by the interplay of multiple structural components, reveal a finely tuned mechanism for potential regulatory control.


  • Organizational Affiliation

    Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial transcription factor 1A [auth B]354Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTF1YMR228WYM9959.10
EC: 2.1.1
UniProt
Find proteins for P14908 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14908 
Go to UniProtKB:  P14908
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UniProt GroupP14908
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase, mitochondrialB [auth A]1,262Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO41YFL036W
EC: 2.7.7.6
UniProt
Find proteins for P13433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P13433 
Go to UniProtKB:  P13433
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UniProt GroupP13433
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Entity ID: 3
MoleculeChains LengthOrganismImage
Non-template DNA (37-mer)C [auth N]37Saccharomyces cerevisiae S288C
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Entity ID: 4
MoleculeChains LengthOrganismImage
Template DNA (37-MER)D [auth T]37Saccharomyces cerevisiae S288C
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (pppGpGpUpApApApUpG)E [auth C]7Saccharomyces cerevisiae S288C
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
F [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX1.19

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
KU LeuvenBelgium--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Database references