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- PDB-36ht: Retron-Kva2 Complex Composite -

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Basic information

Entry
Database: PDB / ID: 36ht
TitleRetron-Kva2 Complex Composite
Components
  • Retron-Kva2 HEPN
  • Retron-Kva2 Reverse Transcriptase
  • Retron-Kva2 WH
  • Retron-Kva2 msdDNA
  • Retron-Kva2 msrRNA
KeywordsIMMUNE SYSTEM / Retron / Reverse transcriptase / Bacterial immune system / Abi / Ribonuclease
Function / homology: / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesKlebsiella variicola (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHibshman, G.N.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: bioRxiv / Year: 2026
Title: Higher-order assembly of a type IX retron enables exploitation for designer antimicrobials.
Authors: Grace N Hibshman / Linhan Wang / Nicole MacRae / Karen Zhang / Alfredo Florez / Seth L Shipman / Eva Nogales /
Abstract: Bacterial defense systems provide a rich reservoir for biotechnological innovation. Retrons are tripartite abortive infection systems that detect phage invasion using reverse-transcribed DNA (msDNA), ...Bacterial defense systems provide a rich reservoir for biotechnological innovation. Retrons are tripartite abortive infection systems that detect phage invasion using reverse-transcribed DNA (msDNA), but how they structurally couple threat detection to effector activation remains poorly understood. Here, we determine the cryo-EM structure and activation mechanism of retron-Kva2, a type IX retron from the human pathogen . We reveal that retron-Kva2 assembles into an asymmetric, higher-order ribonucleoprotein complex that sequesters a toxic dimeric HEPN RNase at its core. We identify a natural phage trigger as the phage T5 protein D5, which activates the retron through structural mimicry. Mirroring the retron-Kva2 winged-helix protein, the helix-turn-helix fold of D5 binds the msDNA sensor, driving conformational remodeling that unleashes HEPN-mediated tRNA cleavage and growth arrest. Because retron-Kva2 surveils a structural fold via msDNA binding, rather than a primary sequence, this recognition mechanism provides a broadly exploitable pathway for programmable activation. Harnessing this structure-based logic, we computationally designed synthetic triggers that activate retron-Kva2-mediated bacterial growth arrest . Our findings reveal the architectural basis of type IX retron immunity and establish a structure-guided paradigm for repurposing bacterial defense systems into precision-honed antimicrobial therapeutics.
History
DepositionJun 10, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retron-Kva2 Reverse Transcriptase
B: Retron-Kva2 WH
C: Retron-Kva2 msdDNA
D: Retron-Kva2 msrRNA
E: Retron-Kva2 Reverse Transcriptase
G: Retron-Kva2 msdDNA
H: Retron-Kva2 msrRNA
I: Retron-Kva2 HEPN
J: Retron-Kva2 Reverse Transcriptase
K: Retron-Kva2 msrRNA
L: Retron-Kva2 WH
M: Retron-Kva2 HEPN
N: Retron-Kva2 msdDNA
O: Retron-Kva2 msdDNA
F: Retron-Kva2 WH


Theoretical massNumber of molelcules
Total (without water)503,90915
Polymers503,90915
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Retron-Kva2 Reverse Transcriptase


Mass: 37382.836 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella variicola (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Retron-Kva2 WH


Mass: 28262.975 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella variicola (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: DNA chain
Retron-Kva2 msdDNA


Mass: 25283.123 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella variicola (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: GenBank: 1142867176
#4: RNA chain Retron-Kva2 msrRNA


Mass: 55655.980 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella variicola (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: GenBank: 1142867176
#5: Protein Retron-Kva2 HEPN


Mass: 19435.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella variicola (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Higher order assembly of retron Kva2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.397 MDa / Experimental value: YES
Source (natural)Organism: Klebsiella variicola (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 663948 / Symmetry type: POINT
RefinementHighest resolution: 3.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00623922
ELECTRON MICROSCOPYf_angle_d1.15933837
ELECTRON MICROSCOPYf_dihedral_angle_d25.856172
ELECTRON MICROSCOPYf_chiral_restr0.0613915
ELECTRON MICROSCOPYf_plane_restr0.0083063

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