[English] 日本語
Yorodumi
- EMDB-62378: Cryo-EM structure of the Retron-Eco7 complex (state 1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62378
TitleCryo-EM structure of the Retron-Eco7 complex (state 1)
Map data
Sample
  • Complex: Retron-Eco7 complex (state 1)
    • Protein or peptide: RNA-directed DNA polymerase
    • Protein or peptide: AAA family ATPase
    • Protein or peptide: TIGR02646 family protein
    • RNA: msrRNA
    • DNA: msdDNA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsRetron / Reverse transcriptase / RNA BINDING PROTEIN
Function / homology:
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsIshikawa J / Yoneyama K / Yamashita K / Nishimasu H
Funding support Japan, 3 items
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, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_62378.png

Downloads & links

-
Map

FileDownload / File: emd_62378.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 400 pix.
= 398.4 Å		1 Å/pix.
x 400 pix.
= 398.4 Å		1 Å/pix.
x 400 pix.
= 398.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.996 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.5667909 - 1.0030968
Average (Standard dev.)-0.00006872833 (±0.019139314)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 398.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_62378_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62378_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62378_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Retron-Eco7 complex (state 1)

EntireName: Retron-Eco7 complex (state 1)
Components
  • Complex: Retron-Eco7 complex (state 1)
    • Protein or peptide: RNA-directed DNA polymerase
    • Protein or peptide: AAA family ATPase
    • Protein or peptide: TIGR02646 family protein
    • RNA: msrRNA
    • DNA: msdDNA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Retron-Eco7 complex (state 1)

SupramoleculeName: Retron-Eco7 complex (state 1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: RNA-directed DNA polymerase

MacromoleculeName: RNA-directed DNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 36.682363 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHGG GSSVIRGLAA VLRQSDSDIS AFLVTAPRKY KVYKIPKRTT GFRVIAQPAK GLKDIQRAFV QLYSLPVHDA SMAYMKGKG IRDNAAAHAG NQYLLKADLE DFFNSITPAI FWRCIEMSSA QTPQFEPQDK LFIEKILFWQ PIKRRKTKLI L SVGAPSSP ...String:
MGHHHHHHGG GSSVIRGLAA VLRQSDSDIS AFLVTAPRKY KVYKIPKRTT GFRVIAQPAK GLKDIQRAFV QLYSLPVHDA SMAYMKGKG IRDNAAAHAG NQYLLKADLE DFFNSITPAI FWRCIEMSSA QTPQFEPQDK LFIEKILFWQ PIKRRKTKLI L SVGAPSSP VISNFCMYEF DNRIHAACKK VEITYTRYAD DLTFSSNIPD VLKAVPSTLE VLLKDLFGSA LRLNHSKTVF SS KAHNRHV TGITINNEET LSLGRDRKRF IKHLINQYKY GLLDNEDKAY LIGLLAFASH IEPSFITRMN EKYSLELMER LRG QR

-
Macromolecule #2: AAA family ATPase

MacromoleculeName: AAA family ATPase / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 62.467766 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTKQYERKAK GGNLLSAFEL YQRNSDKAPG LGEMLVGEWF EMCRDYIQDG HVDESGIFRP DNAFYLRRLT LKDFRRFSLL EIKLEEDLT VIIGNNGKGK TSILYAIAKT LSWFVANILK EGGSGQRLSE MTDIKNDAED RYSDVSSTFF FGKGLKSVPI R LSRSALGT ...String:
MTKQYERKAK GGNLLSAFEL YQRNSDKAPG LGEMLVGEWF EMCRDYIQDG HVDESGIFRP DNAFYLRRLT LKDFRRFSLL EIKLEEDLT VIIGNNGKGK TSILYAIAKT LSWFVANILK EGGSGQRLSE MTDIKNDAED RYSDVSSTFF FGKGLKSVPI R LSRSALGT AERRDSEVKP AKDLADIWRV INEVNTINLP TFALYNVERS QPFNRNIKDN TGRREERFDA YSQTLGGAGR FD HFVEWYI YLHKRTVSDI SSSIKELEQQ VNDLQRTVDG GMVSVKSLLE QMKFKLSEAI ERNDAAVSSR VLTESVQKSI VEK AICSVV PSISNIWVEM ITGSDLVKVT NDGHDVTIDQ LSDGQRVFLS LVADLARRMV MLNPLLENPL EGRGIVLIDE IELH LHPKW QQEVILNLRS AFPNIQFIIT THSPIVLSTI EKRCIREFEP NDDGDQSFLD SPDMQTKGSE NAQILEQVMN VHSTP PGIA ESHWLGNFEL LLLDNSGELD NHSQVLYDQI KAHFGIDSIE LKKADSLIRI NKMKNKLNKI RAEKGK

UniProtKB: UNIPROTKB: A0AAW7FAT4

-
Macromolecule #3: TIGR02646 family protein

MacromoleculeName: TIGR02646 family protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 29.739086 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRELARLERP EILDQYIAGQ NDWMEIDQSA VWPKLTEMQG GFCAYCECRL NRCHIEHFRP RGKFPALTFI WNNLFGSCGD SRKSGGWSR CGIYKDNGAG AYNADDLIKP DEENPDDYLL FLTTGEVVPA IGLTGRALKK AQETIRVFNL NGDIKLFGSR R TAVQAIMP ...String:
MRELARLERP EILDQYIAGQ NDWMEIDQSA VWPKLTEMQG GFCAYCECRL NRCHIEHFRP RGKFPALTFI WNNLFGSCGD SRKSGGWSR CGIYKDNGAG AYNADDLIKP DEENPDDYLL FLTTGEVVPA IGLTGRALKK AQETIRVFNL NGDIKLFGSR R TAVQAIMP NVEYLYTLLE EFDEDDWNEM LRDELEKIES DEYKTALKHA WTFNQEFAGG GSGGGSSSGL VPRGSHMASW SH PQFEKGG GSGGGSGGSA WSHPQFEKN

-
Macromolecule #4: msrRNA

MacromoleculeName: msrRNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 46.843566 KDa
SequenceString:
GGACUCUUUA GCGUUGGACG GUUACGUCUA GUCGGGUGAU UAGCCAGACU CUAACUUAUU GAACGUAUUA AGGGUUGCGA AAGUGUCGC AACCCGAGAU CGUUCCUCUC UCGGGUUGCG ACACUUUCGC UUCCUCAAGU AAAGAGU

-
Macromolecule #5: msdDNA

MacromoleculeName: msdDNA / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.807242 KDa
SequenceString: (DT)(DT)(DG)(DA)(DG)(DG)(DA)(DA)(DG)(DC) (DG)(DA)(DA)(DA)(DG)(DT)(DG)(DT)(DC)(DG) (DC)(DA)(DA)(DC)(DC)(DC)(DG)(DA)(DG) (DA)(DG)(DA)(DG)(DG)(DA)(DA)(DC)(DG)(DA) (DT) (DC)(DT)(DC)(DG)(DG)(DG) ...String:
(DT)(DT)(DG)(DA)(DG)(DG)(DA)(DA)(DG)(DC) (DG)(DA)(DA)(DA)(DG)(DT)(DG)(DT)(DC)(DG) (DC)(DA)(DA)(DC)(DC)(DC)(DG)(DA)(DG) (DA)(DG)(DA)(DG)(DG)(DA)(DA)(DC)(DG)(DA) (DT) (DC)(DT)(DC)(DG)(DG)(DG)(DT)(DT) (DG)(DC)(DG)(DA)(DC)(DA)(DC)(DT)(DT)(DT) (DC)(DG) (DC)(DA)(DA)(DC)(DC)(DC)(DT) (DT)(DA)(DA)(DT)(DA)(DC)(DG)(DT)(DT)(DC)

GENBANK: GENBANK: U02551.1

-
Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 3 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

-
Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 67250
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more