9N6C | pdb_00009n6c

Structure of the Retron IA Complex without the HNH Nuclease


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis of antiphage defense by an ATPase-associated reverse transcriptase.

George, J.T.Burman, N.Wilkinson, R.A.de Silva, S.McKelvey-Pham, Q.Buyukyoruk, M.Dale, A.Landman, H.Graham, A.DeLuca, S.Z.Wiedenheft, B.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.03.26.645336
  • Primary Citation of Related Structures:  
    9N69, 9N6B, 9N6C

  • PubMed Abstract: 

    Reverse transcriptases (RTs) have well-established roles in the replication and spread of retroviruses and retrotransposons. However, recent evidence suggests that RTs have been conscripted by cells for diverse roles in antiviral defense. Here we determine structures of a type I-A retron, which explain how RNA, DNA, RT, HNH-nuclease and four molecules of an SMC-family ATPase assemble into a 364 kDa complex that provides phage defense. We show that phage-encoded nucleases trigger degradation of the retron-associated DNA, leading to disassembly of the retron and activation of the HNH nuclease. The HNH nuclease cleaves tRNA Ser , stalling protein synthesis and arresting viral replication. Taken together, these data reveal diverse and paradoxical roles for RTs in the perpetuation and elimination of genetic parasites.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AAA family ATPase
A, B, C, D
552Escherichia coliMutation(s): 0 
Gene Names: QY721_001703
UniProt
Find proteins for A0AAD2V6K7 (Escherichia coli O33)
Explore A0AAD2V6K7 
Go to UniProtKB:  A0AAD2V6K7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAD2V6K7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed DNA polymerase311Escherichia coliMutation(s): 0 
Gene Names: QY721_001704
EC: 2.7.7.49
UniProt
Find proteins for A0AAD2V6H6 (Escherichia coli O33)
Explore A0AAD2V6H6 
Go to UniProtKB:  A0AAD2V6H6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAD2V6H6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
Retron IA msDNAF [auth H]162Escherichia coli
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
Retron IA ncRNAG [auth I]162Escherichia coli
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv4.6.2
MODEL REFINEMENTISOLDE1.6.0
MODEL REFINEMENTPHENIX1.21.2-5419

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 States5F31GM153146-02
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R35GM134867

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release