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- EMDB-77585: Retron-Kva2 Complex Composite -

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Basic information

Entry
Database: EMDB / ID: EMD-77585
TitleRetron-Kva2 Complex Composite
Map data
Sample
  • Complex: Higher order assembly of retron Kva2
    • Protein or peptide: Retron-Kva2 Reverse Transcriptase
    • Protein or peptide: Retron-Kva2 WH
    • DNA: Retron-Kva2 msdDNA
    • RNA: Retron-Kva2 msrRNA
    • Protein or peptide: Retron-Kva2 HEPN
KeywordsRetron / Reverse transcriptase / Bacterial immune system / Abi / Ribonuclease / IMMUNE SYSTEM
Biological speciesKlebsiella variicola (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHibshman GN
Funding support United States, 1 items
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, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77585.png

Downloads & links

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Map

FileDownload / File: emd_77585.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.14 Å/pix.
x 420 pix.
= 478.8 Å		1.14 Å/pix.
x 420 pix.
= 478.8 Å		1.14 Å/pix.
x 420 pix.
= 478.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.27
Minimum - Maximum-13.864661 - 161.415899999999993
Average (Standard dev.)0.0075515397 (±1.1947476)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 478.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Higher order assembly of retron Kva2

EntireName: Higher order assembly of retron Kva2
Components
  • Complex: Higher order assembly of retron Kva2
    • Protein or peptide: Retron-Kva2 Reverse Transcriptase
    • Protein or peptide: Retron-Kva2 WH
    • DNA: Retron-Kva2 msdDNA
    • RNA: Retron-Kva2 msrRNA
    • Protein or peptide: Retron-Kva2 HEPN

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Supramolecule #1: Higher order assembly of retron Kva2

SupramoleculeName: Higher order assembly of retron Kva2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Klebsiella variicola (bacteria)
Molecular weightTheoretical: 397 KDa

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Macromolecule #1: Retron-Kva2 Reverse Transcriptase

MacromoleculeName: Retron-Kva2 Reverse Transcriptase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella variicola (bacteria)
Molecular weightTheoretical: 37.382836 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKTPLPLLFS YNDAQQFLGA LSPEVRDVYS PEINRLFDRG LPPVVSWSVL SVAIGVSPHF INSIIKNKDK YYRIFPIAKG KGKKVRIIE SPRVGLKIIQ SWLAHHLATN DNIPVSDSAY AFIPGKNGIY EAAFRHCNAK WVLSIDLRDF FHSIDFDRVI N GLRNTGYT ...String:
MKTPLPLLFS YNDAQQFLGA LSPEVRDVYS PEINRLFDRG LPPVVSWSVL SVAIGVSPHF INSIIKNKDK YYRIFPIAKG KGKKVRIIE SPRVGLKIIQ SWLAHHLATN DNIPVSDSAY AFIPGKNGIY EAAFRHCNAK WVLSIDLRDF FHSIDFDRVI N GLRNTGYT FEQSGKIAAI VTYKNRLPQG APSSPVLSNI VFKDTDDKIN DIIADKKIIY TRYADDLTFS SDDLSIDVEN LK QNIINLL ENENWTIATE KLKISKIPNR LKVHGFLVHD VKPRLTKGYR NKLRTYEHLL RNGKIIESDL NRIRGHVNYG KHI DKLNDE N

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Macromolecule #2: Retron-Kva2 WH

MacromoleculeName: Retron-Kva2 WH / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella variicola (bacteria)
Molecular weightTheoretical: 28.262975 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MYSKEMLEYI LGKYPIISVR EVNDFSETIL LDIPINRLSP AAKNGFITKR QVSNITKKIE SELSVKVLVS YSTSQSKLDI EAGLKALAK ANFKGKKIID LDVSFEDVKN ASVYIFSMNM SDEDKEKWGL LAGDYFSSLN IKLNALMYEQ KNNPEPTLMI M LRTMKILY ...String:
MYSKEMLEYI LGKYPIISVR EVNDFSETIL LDIPINRLSP AAKNGFITKR QVSNITKKIE SELSVKVLVS YSTSQSKLDI EAGLKALAK ANFKGKKIID LDVSFEDVKN ASVYIFSMNM SDEDKEKWGL LAGDYFSSLN IKLNALMYEQ KNNPEPTLMI M LRTMKILY PCDLPTMKKA LEDKEYHIES SDWLNKKLDS LRKKNLIIRD REGTYRMTYL GLELVPVTRS KQSSDVDRIL YL AKKHL

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Macromolecule #5: Retron-Kva2 HEPN

MacromoleculeName: Retron-Kva2 HEPN / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella variicola (bacteria)
Molecular weightTheoretical: 19.43568 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MTALYEVAEH LTKQAKASHR KGAQTIVLAD AFARSAFNRY YYACFLCIRT FVSSIEAKWS NVAHLDVPNL LRNNVKQKID AELKKGEKI GILTPGGYQS KKSMVLTSLE IMASTMSLAY IVRGIVDYEP EIKIMFNEGA FSINATSVAE AKGWLMTIKT E EAKIKRIL QEVGIV

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Macromolecule #3: Retron-Kva2 msdDNA

MacromoleculeName: Retron-Kva2 msdDNA / type: dna / ID: 3 / Number of copies: 4 / Classification: DNA
Source (natural)Organism: Klebsiella variicola (bacteria)
Molecular weightTheoretical: 25.283123 KDa
SequenceString: (DG)(DT)(DT)(DG)(DA)(DT)(DG)(DA)(DC)(DG) (DC)(DC)(DT)(DG)(DT)(DG)(DA)(DA)(DG)(DC) (DA)(DG)(DC)(DA)(DG)(DG)(DC)(DG)(DT) (DT)(DT)(DC)(DG)(DA)(DA)(DG)(DG)(DA)(DG) (DC) (DG)(DC)(DC)(DT)(DG)(DC) ...String:
(DG)(DT)(DT)(DG)(DA)(DT)(DG)(DA)(DC)(DG) (DC)(DC)(DT)(DG)(DT)(DG)(DA)(DA)(DG)(DC) (DA)(DG)(DC)(DA)(DG)(DG)(DC)(DG)(DT) (DT)(DT)(DC)(DG)(DA)(DA)(DG)(DG)(DA)(DG) (DC) (DG)(DC)(DC)(DT)(DG)(DC)(DT)(DG) (DC)(DT)(DT)(DC)(DA)(DC)(DA)(DG)(DG)(DC) (DG)(DC) (DA)(DC)(DA)(DT)(DT)(DC)(DT) (DG)(DT)(DA)(DC)(DG)(DC)(DG)(DA)(DC)(DC) (DT)(DT)(DC) (DA)(DC)

GENBANK: GENBANK: CP017284.1

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Macromolecule #4: Retron-Kva2 msrRNA

MacromoleculeName: Retron-Kva2 msrRNA / type: rna / ID: 4 / Number of copies: 3
Source (natural)Organism: Klebsiella variicola (bacteria)
Molecular weightTheoretical: 55.65598 KDa
SequenceString:
GGUAGUGGCG UUCACGAGGG UGUGUAUCAU ACCCAUUUGU GAAGGUCGCG UACAGAAUGU GCGCCUGUGA AGCAGCAGGC GCUCCUUCG AAACGCCUGC UGCUUCACAG GCGUCAUCAA CGAAAGCCUC AUCAGCUUUG CUUAAGGACU GACCUGGAUG A AAACGCCA CUACC

GENBANK: GENBANK: CP017284.1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 663948
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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