[English] 日本語
Yorodumi
- EMDB-49575: Cryo-EM structure of the Retron Ec78 complex, PtuA:PtuB:RT (4:2:2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49575
TitleCryo-EM structure of the Retron Ec78 complex, PtuA:PtuB:RT (4:2:2)
Map data
Sample
  • Complex: Retron Ec78 complex
    • Protein or peptide: Retron I-A effector PtuA
    • Protein or peptide: Retron I-A effector PtuB
    • Protein or peptide: Retron I-A Ec78 reverse transcriptase
    • DNA: DNA (73-MER)
    • RNA: RNA (41-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsRetron / ncRNA / msDNA / DNA-RNA HYBRID
Function / homology
Function and homology information


DNA synthesis involved in DNA repair / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / double-strand break repair / endonuclease activity / defense response to virus / ATP hydrolysis activity / RNA binding / ATP binding
Similarity search - Function
: / : / Retron Ec78 putative HNH endonuclease-like / AAA domain, putative AbiEii toxin, Type IV TA system / RNA-directed DNA polymerase (reverse transcriptase), msDNA / : / ATPase, AAA-type, core / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. ...: / : / Retron Ec78 putative HNH endonuclease-like / AAA domain, putative AbiEii toxin, Type IV TA system / RNA-directed DNA polymerase (reverse transcriptase), msDNA / : / ATPase, AAA-type, core / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA-directed DNA polymerase / Retron Ec78 probable ATPase / Retron Ec78 putative HNH endonuclease
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsWang B / Li H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis for retron co-option of anti-phage ATPase-nuclease.
Authors: Bing Wang / Renee D Hoffman / Ya-Ming Hou / Hong Li /
Abstract: Retrons have been recently identified as bacterial defense systems that employ a tripartite of reverse transcriptase, non-coding RNA (ncRNA) and its derived multi-copy single stranded DNA (msDNA) to ...Retrons have been recently identified as bacterial defense systems that employ a tripartite of reverse transcriptase, non-coding RNA (ncRNA) and its derived multi-copy single stranded DNA (msDNA) to sequester effector activity. Phage invasion activates retrons, triggering effector activity and inducing abortive infection and cell growth arrest. Ec78 differs from other retrons by leveraging the Septu defense system, a stand-alone ATPase-nuclease pair (PtuAB), by reshaping the phage sensing and molecular assembly processes of PtuAB. To elucidate how Ec78 hijacks PtuAB, we determined electron cryomicroscopy structures of Ec78 as well as the retron-displaced PtuAB. We show that the Ec78-associated ATPase, PtuA, acquired unique elements that enable its interactions with the reverse transcriptase and the msDNA, and self-assembly when displaced by the retron. By biochemical and mutational analyses, we also show that the retron-displaced PtuAB forms a tetramer, unlike its stand-alone counterpart, that restricts the host. However, in the presence of the retron, the retron-displaced PtuAB confers a well-controlled immune response, eliciting ATP hydrolysis- and msDNA-regulated targeting to host factors. Our studies reveal an evolutionary principle for retrons to co-opt conserved enzyme modules for defense in response to different cellular needs.
History
DepositionMar 5, 2025-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49575.png

Downloads & links

-
Map

FileDownload / File: emd_49575.map.gz / Format: CCP4 / Size: 172.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 356 pix.
= 294.768 Å		0.83 Å/pix.
x 356 pix.
= 294.768 Å		0.83 Å/pix.
x 356 pix.
= 294.768 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21
Minimum - Maximum-1.1826681 - 2.166041
Average (Standard dev.)0.0030343789 (±0.05206558)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions356356356
Spacing356356356
CellA=B=C: 294.768 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_49575_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_49575_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Retron Ec78 complex

EntireName: Retron Ec78 complex
Components
  • Complex: Retron Ec78 complex
    • Protein or peptide: Retron I-A effector PtuA
    • Protein or peptide: Retron I-A effector PtuB
    • Protein or peptide: Retron I-A Ec78 reverse transcriptase
    • DNA: DNA (73-MER)
    • RNA: RNA (41-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

-
Supramolecule #1: Retron Ec78 complex

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

-
Macromolecule #1: Retron I-A effector PtuA

MacromoleculeName: Retron I-A effector PtuA / type: protein_or_peptide / ID: 1 / 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: Retron Ec78 probable ATPase

-
Macromolecule #2: Retron I-A effector PtuB

MacromoleculeName: Retron I-A effector PtuB / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 26.879172 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 WTFNQEFALE VLFQGPEAHH HHHH

UniProtKB: Retron Ec78 putative HNH endonuclease

-
Macromolecule #3: Retron I-A Ec78 reverse transcriptase

MacromoleculeName: Retron I-A Ec78 reverse transcriptase / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 35.538195 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSVIRGLAAV LRQSDSDISA FLVTAPRKYK VYKIPKRTTG FRVIAQPAKG LKDIQRAFVQ LYSLPVHDAS MAYMKGKGIR DNAAAHAGN QYLLKADLED FFNSITPAIF WRCIEMSSAQ TPQFEPQDKL FIEKILFWQP IKRRKTKLIL SVGAPSSPVI S NFCMYEFD ...String:
MSVIRGLAAV LRQSDSDISA FLVTAPRKYK VYKIPKRTTG FRVIAQPAKG LKDIQRAFVQ LYSLPVHDAS MAYMKGKGIR DNAAAHAGN QYLLKADLED FFNSITPAIF WRCIEMSSAQ TPQFEPQDKL FIEKILFWQP IKRRKTKLIL SVGAPSSPVI S NFCMYEFD NRIHAACKKV EITYTRYADD LTFSSNIPDV LKAVPSTLEV LLKDLFGSAL RLNHSKTVFS SKAHNRHVTG IT INNEETL SLGRDRKRFI KHLINQYKYG LLDNEDKAYL IGLLAFASHI EPSFITRMNE KYSLELMERL RGQR

UniProtKB: RNA-directed DNA polymerase

-
Macromolecule #4: DNA (73-MER)

MacromoleculeName: DNA (73-MER) / type: dna / ID: 4 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.120449 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) (DA)

-
Macromolecule #5: RNA (41-MER)

MacromoleculeName: RNA (41-MER) / type: rna / ID: 5 / Number of copies: 2
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 21.425598 KDa
SequenceString:
ACUCUUUAGC GUUGGACGGU UACGUCUAGU CGGGUGAUUA GCCAGACUCU AACUUAUUGA ACGUAUU

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k 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: OTHER / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 301183
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9nnh:
Cryo-EM structure of the Retron Ec78 complex, PtuA:PtuB:RT (4:2:2)

+
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