6YMV

Cryo-EM structure of yeast mitochondrial RNA polymerase partially-melted transcription initiation complex (PmIC)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Cryo-EM Structures Reveal Transcription Initiation Steps by Yeast Mitochondrial RNA Polymerase.

De Wijngaert, B.Sultana, S.Singh, A.Dharia, C.Vanbuel, H.Shen, J.Vasilchuk, D.Martinez, S.E.Kandiah, E.Patel, S.S.Das, K.

(2021) Mol Cell 81: 268

  • DOI: https://doi.org/10.1016/j.molcel.2020.11.016
  • Primary Citation of Related Structures:  
    6YMV, 6YMW

  • PubMed Abstract: 

    Mitochondrial RNA polymerase (mtRNAP) is crucial in cellular energy production, yet understanding of mitochondrial DNA transcription initiation lags that of bacterial and nuclear DNA transcription. We report structures of two transcription initiation intermediate states of yeast mtRNAP that explain promoter melting, template alignment, DNA scrunching, abortive synthesis, and transition into elongation. In the partially melted initiation complex (PmIC), transcription factor MTF1 makes base-specific interactions with flipped non-template (NT) nucleotides "AAGT" at -4 to -1 positions of the DNA promoter. In the initiation complex (IC), the template in the expanded 7-mer bubble positions the RNA and NTP analog UTPαS, while NT scrunches into an NT loop. The scrunched NT loop is stabilized by the centrally positioned MTF1 C-tail. The IC and PmIC states coexist in solution, revealing a dynamic equilibrium between two functional states. Frequent scrunching/unscruching transitions and the imminent steric clashes of the inflating NT loop and growing RNA:DNA with the C-tail explain abortive synthesis and transition into elongation.


  • Organizational Affiliation

    Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14908
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13433
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (33-MER) NON-TEMPLATEC [auth N]33Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (33-MER) templateD [auth T]33Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.08
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
KU LeuvenBelgiumKU Leuven start-up grant

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references
  • Version 1.2: 2020-12-16
    Changes: Database references
  • Version 1.3: 2021-02-03
    Changes: Database references
  • Version 1.4: 2023-10-18
    Changes: Data collection, Database references, Refinement description