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- PDB-9kjz: Cryo-EM structure of the Retron-Eco7 complex (state 3) -

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Entry
Database: PDB / ID: 9kjz
TitleCryo-EM structure of the Retron-Eco7 complex (state 3)
Components
  • AAA family ATPase
  • RNA-directed DNA polymerase
  • TIGR02646 family protein
  • msdDNA
  • msrRNA
KeywordsRNA BINDING PROTEIN / Retron / Reverse transcriptase
Function / homologyADENOSINE-5'-DIPHOSPHATE / : / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsIshikawa, J. / Yoneyama, K. / Yamashita, K. / Nishimasu, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23KJ0720 Japan
Japan Society for the Promotion of Science (JSPS)21H05281 Japan
Japan Society for the Promotion of Science (JSPS)22H00403 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Structural mechanism of the Retron-Eco7 anti-phage defense system.
Authors: Junichiro Ishikawa / Kanta Yoneyama / Aa Haeruman Azam / Asuteka Nagao / Yoshihisa Mitsuda / Ren Nakazaki / Kotaro Chihara / Masahiro Hiraizumi / Keitaro Yamashita / Tsutomu Suzuki / Kotaro ...Authors: Junichiro Ishikawa / Kanta Yoneyama / Aa Haeruman Azam / Asuteka Nagao / Yoshihisa Mitsuda / Ren Nakazaki / Kotaro Chihara / Masahiro Hiraizumi / Keitaro Yamashita / Tsutomu Suzuki / Kotaro Kiga / Hiroshi Nishimasu /
Abstract: Retrons are prokaryotic genetic elements involved in anti-phage defense and consist of a non-coding RNA, a reverse transcriptase (RT), and various effector proteins. Retron-Eco7 (previously known as ...Retrons are prokaryotic genetic elements involved in anti-phage defense and consist of a non-coding RNA, a reverse transcriptase (RT), and various effector proteins. Retron-Eco7 (previously known as Retron-Ec78) from Escherichia coli encodes two effector proteins (the PtuA ATPase and the PtuB nuclease) and degrades the host tRNA upon phage infection, thereby protecting host cells against invading phages. However, its defense mechanism remains elusive. Here, we report the cryo-electron microscopy (cryo-EM) structures of the Retron-Eco7 complex, comprising the RT, multicopy single-stranded DNA (msDNA), PtuA, and PtuB. The Retron-Eco7 structures reveal that the RT-msDNA complex associates with two PtuA-PtuB complexes, potentially inhibiting their nuclease activity and suppressing bacterial growth arrest prior to phage infection. Furthermore, the phage-encoded D15 nuclease acts as a trigger for the Retron-Eco7 system and cleaves the msDNA bound to the complex, facilitating the dissociation of PtuA-PtuB from RT-msDNA. Our data indicate that msDNA cleavage by D15 is the initial step required for the specific cleavage of the host tRNA by the PtuA-PtuB nuclease, which leads to abortive infection. Overall, this study provides mechanistic insights into the Retron-Eco7 system and highlights the diversity of prokaryotic anti-phage defense mechanisms.
History
DepositionNov 12, 2024Deposition site: PDBJ / Processing site: PDBJ
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed DNA polymerase
B: AAA family ATPase
C: AAA family ATPase
D: AAA family ATPase
E: AAA family ATPase
F: TIGR02646 family protein
G: TIGR02646 family protein
H: msrRNA
I: msdDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)418,11915
Polymers416,6829
Non-polymers1,4376
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 ABCDEFG

#1: Protein RNA-directed DNA polymerase


Mass: 36682.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: D4M65_23810, KQO22_004355 / Production host: Escherichia coli (E. coli) / References: RNA-directed DNA polymerase
#2: Protein
AAA family ATPase


Mass: 62467.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: OGW11_10610 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAW7FAT4
#3: Protein TIGR02646 family protein


Mass: 29739.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: D4M65_23820, KQO22_004357 / Production host: Escherichia coli (E. coli)

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

#4: RNA chain msrRNA


Mass: 46843.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#5: DNA chain msdDNA


Mass: 23807.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 437205

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Non-polymers , 3 types, 6 molecules

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


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: Retron-Eco7 complex (state 3) / Type: COMPLEX / Entity ID: #3, #1-#2, #4-#5 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 49.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
9Servalcatmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95729 / Symmetry type: POINT

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