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- PDB-22et: Cryo-EM structure of Retron Ec78 complex (cis) -

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Basic information

Entry
Database: PDB / ID: 22et
TitleCryo-EM structure of Retron Ec78 complex (cis)
Components
  • DNA (74-MER)
  • PtuA
  • PtuB
  • RNA (66-MER)
  • Retron
KeywordsIMMUNE SYSTEM/DNA/RNA / immune / complex / IMMUNE SYSTEM-DNA-RNA complex
Function / homologyADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsLin, Z. / Guo, M. / Zhu, Y. / Lu, Z. / Huang, Z.
Funding support China, 1items
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, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: PtuA
D: PtuA
B: PtuA
C: PtuA
M: DNA (74-MER)
N: RNA (66-MER)
A: Retron
H: PtuB
F: PtuB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)383,37914
Polymers381,8069
Non-polymers1,5725
Water00
1


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

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Components

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Protein , 3 types, 7 molecules EDBCAHF

#1: Protein
PtuA


Mass: 63089.422 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21 (bacteria)
#4: Protein Retron


Mass: 36231.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21 (bacteria)
#5: Protein PtuB


Mass: 24568.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21 (bacteria)

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DNA chain / RNA chain , 2 types, 2 molecules MN

#2: DNA chain DNA (74-MER)


Mass: 22998.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: msdDNA / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21 (bacteria)
#3: RNA chain RNA (66-MER)


Mass: 21080.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: msrRNA / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21 (bacteria)

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Non-polymers , 3 types, 5 molecules

#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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: Retron Ec78 complex(cis) / Type: COMPLEX / Details: Ec78-cis / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

MicroscopyModel: FEI MORGAGNI
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 272348 / Symmetry type: POINT
RefinementHighest resolution: 2.69 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00526939
ELECTRON MICROSCOPYf_angle_d0.88836916
ELECTRON MICROSCOPYf_dihedral_angle_d22.30310593
ELECTRON MICROSCOPYf_chiral_restr0.0614110
ELECTRON MICROSCOPYf_plane_restr0.0064371

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