8YF5

Cryo EM structure of Komagataella phaffii Rat1-Rai1-Rtt103 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex.

Yanagisawa, T.Murayama, Y.Ehara, H.Goto, M.Aoki, M.Sekine, S.I.

(2024) Nat Commun 15: 7854-7854

  • DOI: https://doi.org/10.1038/s41467-024-52157-0
  • Primary Citation of Related Structures:  
    8YF5, 8YFE, 8YFQ, 8YFR

  • PubMed Abstract: 

    The 5´-3´ exoribonuclease Rat1/Xrn2 is responsible for the termination of eukaryotic mRNA transcription by RNAPII. Rat1 forms a complex with its partner proteins, Rai1 and Rtt103, and acts as a "torpedo" to bind transcribing RNAPII and dissociate DNA/RNA from it. Here we report the cryo-electron microscopy structures of the Rat1-Rai1-Rtt103 complex and three Rat1-Rai1-associated RNAPII complexes (type-1, type-1b, and type-2) from the yeast, Komagataella phaffii. The Rat1-Rai1-Rtt103 structure revealed that Rat1 and Rai1 form a heterotetramer with a single Rtt103 bound between two Rai1 molecules. In the type-1 complex, Rat1-Rai1 forms a heterodimer and binds to the RNA exit site of RNAPII to extract RNA into the Rat1 exonuclease active site. This interaction changes the RNA path in favor of termination (the "pre-termination" state). The type-1b and type-2 complexes have no bound DNA/RNA, likely representing the "post-termination" states. These structures illustrate the termination mechanism of eukaryotic mRNA transcription.


  • Organizational Affiliation

    Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5'-3' exoribonuclease
A, C
1,006Komagataella phaffiiMutation(s): 2 
Gene Names: RAT1PP7435_Chr3-0338
EC: 3.1.13
UniProt
Find proteins for F2QV79 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Explore F2QV79 
Go to UniProtKB:  F2QV79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2QV79
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Decapping nuclease
B, D
384Komagataella phaffiiMutation(s): 2 
Gene Names: RAI1PP7435_Chr1-1057
EC: 3.6.1
UniProt
Find proteins for F2QLF5 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Explore F2QLF5 
Go to UniProtKB:  F2QLF5
Entity Groups  
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UniProt GroupF2QLF5
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Exonuclease Rat1p and Rai1p interacting protein381Komagataella phaffiiMutation(s): 0 
Gene Names: RTT103PP7435_Chr1-0928
UniProt
Find proteins for F2QNA8 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Explore F2QNA8 
Go to UniProtKB:  F2QNA8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2QNA8
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP20H05690

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release