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- EMDB-49570: Cryo-EM structure of the Retron Ec78 complex, PtuA:PtuB:RT (4:2:1) -

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Basic information

Entry
Database: EMDB / ID: EMD-49570
TitleCryo-EM structure of the Retron Ec78 complex, PtuA:PtuB:RT (4:2:1)
Map data
Sample
  • Complex: Rectron Ec78 complex
    • Protein or peptide: Retron I-A effector PtuA
    • Protein or peptide: Retron I-A effector PtuB
    • DNA: DNA (73-MER)
    • Protein or peptide: Retron I-A Ec78 reverse transcriptase
    • RNA: RNA (41-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
KeywordsRetron / msDNA / ncRNA / 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: 2.75 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: To Be Published
Title: Structural Basis for Retron Co-option of Anti-phage ATPase-nuclease
Authors: Wang B / Hou YM / Li H
History
DepositionMar 5, 2025-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49570.png

Downloads & links

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Map

FileDownload / File: emd_49570.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: 0.2
Minimum - Maximum-1.367957 - 2.4951959
Average (Standard dev.)0.0018894497 (±0.055176724)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #1

Fileemd_49570_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49570_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rectron Ec78 complex

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

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Supramolecule #1: Rectron Ec78 complex

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

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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: 62.466781 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 EGRGIVLIDQ IELH LHPKW QQEVILNLRS AFPNIQFIIT THSPIVLSTI EKRCIREFEP NDDGDQSFLD SPDMQTKGSE NAQILEQVMN VHSTP PGIA ESHWLGNFEL LLLDNSGELD NHSQVLYDQI KAHFGIDSIE LKKADSLIRI NKMKNKLNKI RAEKGK

UniProtKB: Retron Ec78 probable ATPase

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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

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Macromolecule #4: Retron I-A Ec78 reverse transcriptase

MacromoleculeName: Retron I-A Ec78 reverse transcriptase / type: protein_or_peptide / ID: 4 / Number of copies: 1 / 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

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Macromolecule #3: DNA (73-MER)

MacromoleculeName: DNA (73-MER) / type: dna / ID: 3 / Number of copies: 1 / 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)

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Macromolecule #5: RNA (41-MER)

MacromoleculeName: RNA (41-MER) / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 21.425598 KDa
SequenceString:
ACUCUUUAGC GUUGGACGGU UACGUCUAGU CGGGUGAUUA GCCAGACUCU AACUUAUUGA ACGUAUU

GENBANK: GENBANK: U02551.1

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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

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / 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

Concentration3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
250.0 mMNaClsodium cloride
25.0 mMTrisTris
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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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 opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 140378
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9nnb:
Cryo-EM structure of the Retron Ec78 complex, PtuA:PtuB:RT (4:2:1)

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