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- EMDB-62378: Cryo-EM structure of the Retron-Eco7 complex (state 1) -

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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: To Be Published
Title: Cryo-EM structure of the Retron-Eco7 complex
Authors: Ishikawa J / Yoneyama K
History
DepositionNov 12, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62378.png

Downloads & links

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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 °

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Supplemental data

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Mask #1

Fileemd_62378_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62378_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62378_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 : 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

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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)

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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

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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

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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

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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

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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

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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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Macromolecule #8: MAGNESIUM ION

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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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

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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)

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