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- EMDB-68220: Cryo-EM structure of Retron Ec78 complex (trans) -

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Basic information

Entry
Database: EMDB / ID: EMD-68220
TitleCryo-EM structure of Retron Ec78 complex (trans)
Map data
Sample
  • Complex: Retron Ec78 complex(trans)
    • Protein or peptide: Retron
    • Protein or peptide: PtuA
    • Protein or peptide: PtuB
    • DNA: DNA (74-MER)
    • RNA: RNA (66-MER)
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
Keywordsimmune / complex / IMMUNE SYSTEM/DNA/RNA / IMMUNE SYSTEM-DNA-RNA complex
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsLin Z / Guo M / Zhu Y / Lu Z / Huang Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Dual-inhibitory mechanism of the bacterial retron Ec78 antiphage defense system.
Authors: Zhiying Lin / Minghui Guo / Zebin Lu / Yuwei Zhu / Fengxia Zhou / Anqi Zhang / Changyou Guo / Zhiwei Huang /
Abstract: Retrons are prokaryotic defense modules that protect bacteria from phage infection through abortive infection. The retron Ec78 system employs a two-component effector complex PtuAB to execute this ...Retrons are prokaryotic defense modules that protect bacteria from phage infection through abortive infection. The retron Ec78 system employs a two-component effector complex PtuAB to execute this defense. Despite recent advances in structural research, the molecular mechanism by which PtuAB effector is regulated remains unknown. Here, we reveal that PtuAB is subject to a dual-inhibitory mechanism mediated by ATP/ADP and the RT-msDNA antitoxin. ATP/ADP binds nucleotide-binding domain (NBD) of PtuAB and induces the assembly of an inactive tetrameric complex, whereas the RT-msDNA stabilizes an inhibited conformation of Ec78 complex and stimulates ATP turnover to prime PtuAB for rapid activation. Structural analyses show that RT-msDNA dissociation and nucleotide release from PtuA induce conformational rearrangements in the NBD of PtuA and a downward displacement of a key β-loop-β motif, driving disassembly of the PtuAB tetramer through an allosteric mechanism and thereby activating its tRNA cleavage activity. Our findings uncover how nucleotides-specifically ATP and ADP-regulate the activity of this abortive infection system, and establish a dual-inhibition model of retron Ec78 system, expanding the understanding of the regulation mechanism of PtuAB activation in prokaryotic immune systems.
History
DepositionJan 8, 2026-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68220.png

Downloads & links

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Map

FileDownload / File: emd_68220.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 300 pix.
= 288. Å		0.96 Å/pix.
x 300 pix.
= 288. Å		0.96 Å/pix.
x 300 pix.
= 288. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.4941654 - 1.5418148
Average (Standard dev.)0.003759783 (±0.046521638)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 288.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68220_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_68220_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Retron Ec78 complex(trans)

EntireName: Retron Ec78 complex(trans)
Components
  • Complex: Retron Ec78 complex(trans)
    • Protein or peptide: Retron
    • Protein or peptide: PtuA
    • Protein or peptide: PtuB
    • DNA: DNA (74-MER)
    • RNA: RNA (66-MER)
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: Retron Ec78 complex(trans)

SupramoleculeName: Retron Ec78 complex(trans) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Retron

MacromoleculeName: Retron / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 36.231957 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MSVISSIATS LNQSELEVRA YLSDASGKYK VYRIPKRTTG FRIIAQPAKA LKEYQRTFLQ LYRFPIHECA MAYQKGKSIR DNALAHAHN RYLLKTDLED FFNSITPDIF WRCVELSSVD VQLFLPEDRR YVDQILFWKP TKRSTRLVLS VGAPSSPIIS N FCLYEFDK ...String:
MSVISSIATS LNQSELEVRA YLSDASGKYK VYRIPKRTTG FRIIAQPAKA LKEYQRTFLQ LYRFPIHECA MAYQKGKSIR DNALAHAHN RYLLKTDLED FFNSITPDIF WRCVELSSVD VQLFLPEDRR YVDQILFWKP TKRSTRLVLS VGAPSSPIIS N FCLYEFDK LIHEICRSLD IVYTRYADDL TFSCNVRDVL GSIPSMIETL LNKLFKKKLR LNRGKTIFSS MAHNRHVTGV TL NNEGKIS LGRERKRFIK HLINQYRYGL IDESDKAYLV GLLAFANHIE PEFIIRMNNK YSTETMERLR RHL

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Macromolecule #2: PtuA

MacromoleculeName: PtuA / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 63.089422 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: VTKQLERKAK GGSLLSAFEL YQQEKNNNLH DLNNKSDQWF ELCWNYLQQP AHDGNLDIYH PENQFCLRSM SFTDFRRFPQ LDINFEEDL TIIIGNNGQG KTSILYAIAK TLSWFTANIL KEDSSGQRLN EYSDIRNDSD NNFSDVSSNF FFGKGLKNIS I RLSRSTLG ...String:
VTKQLERKAK GGSLLSAFEL YQQEKNNNLH DLNNKSDQWF ELCWNYLQQP AHDGNLDIYH PENQFCLRSM SFTDFRRFPQ LDINFEEDL TIIIGNNGQG KTSILYAIAK TLSWFTANIL KEDSSGQRLN EYSDIRNDSD NNFSDVSSNF FFGKGLKNIS I RLSRSTLG ASERRESIIK PAKEVADIWR IINERRMVNL PIFALYSVER SHPFSKPAKE SIEKREDRFD AYNHALTGAG RF DHFVEWF IYLHKRAEAQ GASAIELLEE QVNHLKQSVE NGLTSMVPLL EETQKKLLTA QMRKESLQSV NMLTETAQMD IVS RAITTV VPSISRIWVE TASGADIIKV TNDLQDVTIE QLSDGQRVFL ALVADLARRM IMLNPLLKNP LEGRGIVLIA EIEL HLHPK WQQEVIIVLR TVFPNIQFVI TTHSPIVLST TEIRCIREFK QNSESGELFL DSPPIQTKGS ENSDILEQVM GVLST PPNI AESYLVSNFE KSIIDDSEEL SAESRRLYNK IISHFGQHSS ELKKADSLIR LHRMKNKINK AKREKDS

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Macromolecule #3: PtuB

MacromoleculeName: PtuB / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.568682 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MKSLNRTAGP AHLHQFRAGR DPWMSVEQSN IWPHLLEMQG EFCAYCECSL NRKHIEHFRP RGKFPALTFA WGNLFGSCGD SSKTGGWQR CGIFKDNGAG NYNPDHLIKP DDDNPDDYLL FLTTGHVVPA KDISGTKLLK AQETIRVFNL NGDPSLLGSR K KALNYIME ...String:
MKSLNRTAGP AHLHQFRAGR DPWMSVEQSN IWPHLLEMQG EFCAYCECSL NRKHIEHFRP RGKFPALTFA WGNLFGSCGD SSKTGGWQR CGIFKDNGAG NYNPDHLIKP DDDNPDDYLL FLTTGHVVPA KDISGTKLLK AQETIRVFNL NGDPSLLGSR K KALNYIME EVILLHESYE DLGDALWHEM RDAEIQEIGN KEFYTALKHA WLHNSEY

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Macromolecule #4: DNA (74-MER)

MacromoleculeName: DNA (74-MER) / type: dna / ID: 4 / Details: msdDNA / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 22.998736 KDa
SequenceString: (DG)(DG)(DA)(DA)(DG)(DC)(DG)(DA)(DA)(DA) (DG)(DT)(DG)(DT)(DC)(DG)(DC)(DA)(DA)(DC) (DC)(DT)(DG)(DA)(DG)(DG)(DG)(DA)(DG) (DG)(DA)(DA)(DC)(DG)(DA)(DG)(DT)(DG)(DA) (DG) (DG)(DG)(DT)(DT)(DG)(DC) ...String:
(DG)(DG)(DA)(DA)(DG)(DC)(DG)(DA)(DA)(DA) (DG)(DT)(DG)(DT)(DC)(DG)(DC)(DA)(DA)(DC) (DC)(DT)(DG)(DA)(DG)(DG)(DG)(DA)(DG) (DG)(DA)(DA)(DC)(DG)(DA)(DG)(DT)(DG)(DA) (DG) (DG)(DG)(DT)(DT)(DG)(DC)(DG)(DA) (DC)(DA)(DC)(DT)(DT)(DT)(DC)(DG)(DC)(DA) (DA)(DC) (DC)(DC)(DT)(DA)(DA)(DA)(DT) (DA)(DC)(DG)(DT)(DT)(DC)(DA)

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Macromolecule #5: RNA (66-MER)

MacromoleculeName: RNA (66-MER) / type: rna / ID: 5 / Details: msrRNA / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 21.080393 KDa
SequenceString:
ACUCUUUAGC GUUGGACGUU UUACGUCUAG UCGGGUGAUU AGCCAGACUC UAACUUAUUG AACGUA

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 8
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI MORGAGNI
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 242458
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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