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- EMDB-57972: Cryo-EM structure of the E. coli DRT10 RT-ncRNA complex, Eco3 sub... -

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Basic information

Entry
Database: EMDB / ID: EMD-57972
TitleCryo-EM structure of the E. coli DRT10 RT-ncRNA complex, Eco3 subtype with dNTPs
Map dataUnsharpened map
Sample
  • Complex: Eco3DRT10 phage defense system from E.coli
    • RNA: ncRNA component of Eco3DRT10 from E.coli.
    • Protein or peptide: Reverse transcriptase
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
Keywordsphage / defense / ncRNA / RT / RNA BINDING PROTEIN
Function / homology:
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHe Q / Ramirez J
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of the E. coli DRT10 RT-ncRNA complex, Eco3 subtype with dNTPs
Authors: He Q / Ramirez J
History
DepositionMay 9, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57972.png

Downloads & links

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Map

FileDownload / File: emd_57972.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 280 pix.
= 297.08 Å		1.06 Å/pix.
x 280 pix.
= 297.08 Å		1.06 Å/pix.
x 280 pix.
= 297.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.04047389 - 0.10375925
Average (Standard dev.)0.000034324967 (±0.002279512)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 297.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_57972_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Post-processed map with relion. Bfactor 50, low pass to 3.3A

Fileemd_57972_additional_1.map
AnnotationPost-processed map with relion. Bfactor 50, low pass to 3.3A
Projections & Slices
AxesZYX

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Histogram

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Additional map: Post-processed map with DeepEmhacer

Fileemd_57972_additional_2.map
AnnotationPost-processed map with DeepEmhacer
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: Half-map 1

Fileemd_57972_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_57972_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Sample components

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Entire : Eco3DRT10 phage defense system from E.coli

EntireName: Eco3DRT10 phage defense system from E.coli
Components
  • Complex: Eco3DRT10 phage defense system from E.coli
    • RNA: ncRNA component of Eco3DRT10 from E.coli.
    • Protein or peptide: Reverse transcriptase
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Eco3DRT10 phage defense system from E.coli

SupramoleculeName: Eco3DRT10 phage defense system from E.coli / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 250 kDa/nm

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Macromolecule #1: ncRNA component of Eco3DRT10 from E.coli.

MacromoleculeName: ncRNA component of Eco3DRT10 from E.coli. / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 43.840742 KDa
SequenceString:
GGAUGGGGCA GGUUUUUCCU CUUGUGCAUG CAAGGGCGGC UCUGAUAAUG AACAGUAAUA UUUUACUGUU GAGCUUAUGC UCACUGAUC CUGCCGGGCA GGAUGUUCAA UGAUUCCAAU AUAUCCUGCC CCUUCCGC

GENBANK: GENBANK: CP055923.1

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Macromolecule #2: Reverse transcriptase

MacromoleculeName: Reverse transcriptase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 52.485805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTASRIFKKS FSKKNLLKVY TEKIKESGAI GIDRIRPSKL DLTIKNEIAF IFEKVNSGNY KFTAYKEKLI SKGANSTPRQ ISIPTARDR ITLRALCECL TEIYPNSRLK LPHTVIDSLK EALNSSLYAE YAKIDLKSFY PSIEHKLIIN AIKNKIRKKE I RQLITSSL ...String:
MTASRIFKKS FSKKNLLKVY TEKIKESGAI GIDRIRPSKL DLTIKNEIAF IFEKVNSGNY KFTAYKEKLI SKGANSTPRQ ISIPTARDR ITLRALCECL TEIYPNSRLK LPHTVIDSLK EALNSSLYAE YAKIDLKSFY PSIEHKLIIN AIKNKIRKKE I RQLITSSL IVPTVSGTTG SKGIPNNTRG VPQGLAISNI LAEISLSNFD DEINKMHDIW YMRYVDDILI LTPKYQATKI AS HIIDKLQ SLNLNPHPLN EENSKSKVGS LDESFNFLGY HIENRELLIK HESILRFESS LARIFTAYRH ALLQAKSKRD KER AVAYCQ WKLNLRITGC VFEGKRLGWV SYFSQITSTA QLRSVNHTIN NLIRRFGLSS EIKPKSLIKT FYELRRGRAE TFKY IPNFD NLHISQKREL VSMWIGKEKE KKLSNSEIER KFKFKIAKSV KELEEDISGI S

UniProtKB: UNIPROTKB: A0A831GQC7

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Macromolecule #3: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: DTP
Molecular weightTheoretical: 491.182 Da
Chemical component information

ChemComp-DTP:
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

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Macromolecule #4: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: DGT
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-DGT:
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

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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: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 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: OTHER / Details: SGD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 235000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD

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