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Basic information

Entry
Database: EMDB / ID: EMD-62954
TitleCryo-EM structure of the Retron-Eco8 complex
Map data
Sample
  • Complex: Heterotetramer Retron-Eco8 complex
    • Protein or peptide: Retron Eco8 reverse transcriptase
    • Protein or peptide: Retron Eco8 OLD nuclease
    • RNA: RNA (83-MER)
    • DNA: DNA (75-MER)
KeywordsRNA BINDING PROTEIN / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-RNA-DNA complex / ANTIVIRAL PROTEIN/RNA/DNA / ANTIVIRAL PROTEIN-RNA-DNA complex
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsZhang JT / Ji CG / Jia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Retron-Eco8 forms a heterotetramer complex to protects bacteria from phage infection
Authors: Jia N / Zhang JT / Ji CG
History
DepositionJan 3, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62954.png

Downloads & links

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Map

FileReleased
Voxel sizeX=Y=Z: 0.827 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.044115584 - 1.73163
Average (Standard dev.)0.0013947173 (±0.023801943)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 380.42 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62954_msk_1.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 : Heterotetramer Retron-Eco8 complex

EntireName: Heterotetramer Retron-Eco8 complex
Components
  • Complex: Heterotetramer Retron-Eco8 complex
    • Protein or peptide: Retron Eco8 reverse transcriptase
    • Protein or peptide: Retron Eco8 OLD nuclease
    • RNA: RNA (83-MER)
    • DNA: DNA (75-MER)

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Supramolecule #1: Heterotetramer Retron-Eco8 complex

SupramoleculeName: Heterotetramer Retron-Eco8 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Retron Eco8 reverse transcriptase

MacromoleculeName: Retron Eco8 reverse transcriptase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 43.273203 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MKTKKMILVD KVFYEKILSV ESFKENIITQ SAIPKISNKE VRLISSGSKI FYAINNTSPH SHVQLRLNRF FLSHIPLNSA AKAFVRGGS YLKYLEPHIY GSSYCRLDIS SFFNNISFDD VKQSLSPYIK DEYLIGTEQK LIDAILNSVG YESPIRKDKG M IIPMGFRT ...String:
MKTKKMILVD KVFYEKILSV ESFKENIITQ SAIPKISNKE VRLISSGSKI FYAINNTSPH SHVQLRLNRF FLSHIPLNSA AKAFVRGGS YLKYLEPHIY GSSYCRLDIS SFFNNISFDD VKQSLSPYIK DEYLIGTEQK LIDAILNSVG YESPIRKDKG M IIPMGFRT SPAISNIVFR KMDLLIQDFC AKKGVIYSRY ADDMLFSNPR ESKLLMSDYF IDEISSLLSI MGFNINQSKY IS REKEISI NGYVIENKGG NGSIGTIRLS KSKLNTVLKV THALAQNIPY KNICNKYIKV RLKEKNIKYE SKKDEFEKKY YRD QLINYL GGYRSYLISL VKFHSEYKCV NSDFIIQING ILNDIQNHIQ KIKKNRRL

UniProtKB: Retron Eco8 reverse transcriptase

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Macromolecule #2: Retron Eco8 OLD nuclease

MacromoleculeName: Retron Eco8 OLD nuclease / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 87.373789 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MTIESIRVKN LLSFDDVILR DFRDINCIIG RNNVGKSNLL KVIRYFYAKL ENKKVIPLDF HTNYNAVGEI TFTFDTTRIK KIVTSRKNN GRFHKHIYNT LFKSSSVKLN FEELIARKNS TNKSFFSLTL TICKDDSVMW SVDDPKVRSL LATLYPFLYI E TRHIDLYD ...String:
MTIESIRVKN LLSFDDVILR DFRDINCIIG RNNVGKSNLL KVIRYFYAKL ENKKVIPLDF HTNYNAVGEI TFTFDTTRIK KIVTSRKNN GRFHKHIYNT LFKSSSVKLN FEELIARKNS TNKSFFSLTL TICKDDSVMW SVDDPKVRSL LATLYPFLYI E TRHIDLYD WNPIWKLISN LNSFNFDDVD HDELVNFLDE KISSRKGDYK KYIDRVVSVI DTKPYTYKEK VINYIKVAIK GD SFVNAGE ELFTQSDGTN SNKFLETLLH LLITLTRTEF ISPIVYIDEP EVGLHPKLAE SFVSNLNKIY SKFKKTSELS GPG RYKTPY PNIFYSTHSP SILKQTIKLF GKDQQVLHFS KKKDGSTRVN KINSTYSDER FLNIFSDNEA RLFFSEYIVF VEGA TELEL FRNLSLLNLY PAFSLADIYD ANEVILANIN PGYSKASIPF VIIKDIDTLI DYSIKTEKFS LRPLFEKMIK ELTKE FDYY DTGFGRVRKE IDLFSDIQSS TKKHMDSGLF FKRFSLHNLS SRINKVSRKL NRYFMTTTIE GALINEQSLP YFFNWI GDV ILTQMTINNP NPDKFIEAMR RRYNIKSQVV PLFKSVFCIG LNHPVYSSAV DKQALRIKLS FLNYLKRKVY SDFNNEK EI VLALRLAFGG KTETQYTLDK LRKDGEAELF REKIKNYKNN ELFFLEPQMT KTSGWVTTFL NYTIEKITSE ESDDDRIR Q KLSFIFPEII SIIEQASSSI EAEESSLTG

UniProtKB: Retron Eco8 OLD nuclease

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Macromolecule #3: RNA (83-MER)

MacromoleculeName: RNA (83-MER) / type: rna / ID: 3 / Number of copies: 4
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 26.660795 KDa
SequenceString:
AGAAGCUUCU UCUUCGAUAG AAGCUGAGGA GUCCAGUUUG ACUGGAUAAG GUGUUCGCCA UCUCUAGCCU CAGUAAAAAC UAG

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Macromolecule #4: DNA (75-MER)

MacromoleculeName: DNA (75-MER) / type: dna / ID: 4 / Number of copies: 4 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.126848 KDa
SequenceString: (DC)(DA)(DA)(DG)(DA)(DC)(DC)(DA)(DA)(DT) (DC)(DT)(DT)(DT)(DA)(DC)(DA)(DC)(DT)(DC) (DT)(DG)(DT)(DG)(DA)(DG)(DT)(DA)(DT) (DT)(DA)(DA)(DA)(DG)(DT)(DT)(DA)(DC)(DC) (DT) (DA)(DT)(DA)(DG)(DC)(DG) ...String:
(DC)(DA)(DA)(DG)(DA)(DC)(DC)(DA)(DA)(DT) (DC)(DT)(DT)(DT)(DA)(DC)(DA)(DC)(DT)(DC) (DT)(DG)(DT)(DG)(DA)(DG)(DT)(DA)(DT) (DT)(DA)(DA)(DA)(DG)(DT)(DT)(DA)(DC)(DC) (DT) (DA)(DT)(DA)(DG)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DT)(DG)(DC)(DG)(DC)(DA)(DA) (DA)(DG) (DG)(DA)(DT)(DG)(DA)(DG)(DC) (DT)(DA)(DG)(DT)(DT)(DT)(DT)(DT)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (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: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 73154
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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