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- EMDB-57959: Cryo-EM structure of the E. coli DRT10 RT-ncRNA complex, Eco1 subtype -

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Basic information

Entry
Database: EMDB / ID: EMD-57959
TitleCryo-EM structure of the E. coli DRT10 RT-ncRNA complex, Eco1 subtype
Map dataRelion unsharpened map
Sample
  • Complex: E. coli DRT10 RT-ncRNA complex
    • RNA: ncRNA component of the Eco1DRT10 E.coli defense system.
    • Protein or peptide: Monomer 1 RT component of the Eco1DRT E.coli defense system.
Keywordsphage. defense / RNA / RNA BINDING PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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: Structural insights into the mechanism of telomerase-like DNA synthesis by an antiviral reverse transcriptase
Authors: Ramirez J / He Q / Fernandez IS / Sternberg SH
History
DepositionMay 8, 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_57959.png

Downloads & links

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Map

FileDownload / File: emd_57959.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRelion unsharpened map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 210 pix.
= 280.98 Å		1.34 Å/pix.
x 210 pix.
= 280.98 Å		1.34 Å/pix.
x 210 pix.
= 280.98 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.338 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.023214545 - 0.062420074
Average (Standard dev.)0.00004891094 (±0.0018693455)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 280.98 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_57959_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Relion post-processed map with auto B option

Fileemd_57959_additional_1.map
AnnotationRelion post-processed map with auto B option
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Additional map: DeepEMhacer post-processed map

Fileemd_57959_additional_2.map
AnnotationDeepEMhacer post-processed map
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AxesZYX

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Half map: Relion half-map 2

Fileemd_57959_half_map_1.map
AnnotationRelion half-map 2
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: Relion half-map 1

Fileemd_57959_half_map_2.map
AnnotationRelion half-map 1
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AxesZYX

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Sample components

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Entire : E. coli DRT10 RT-ncRNA complex

EntireName: E. coli DRT10 RT-ncRNA complex
Components
  • Complex: E. coli DRT10 RT-ncRNA complex
    • RNA: ncRNA component of the Eco1DRT10 E.coli defense system.
    • Protein or peptide: Monomer 1 RT component of the Eco1DRT E.coli defense system.

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Supramolecule #1: E. coli DRT10 RT-ncRNA complex

SupramoleculeName: E. coli DRT10 RT-ncRNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 250 kDa/nm

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Macromolecule #1: ncRNA component of the Eco1DRT10 E.coli defense system.

MacromoleculeName: ncRNA component of the Eco1DRT10 E.coli defense system.
type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 40.233605 KDa
SequenceString:
GAGGCGUAUC GCUAAGCGAU CAUCCAGGUU UACUGGGUGC AACUAAUUUU GGGAGGCUUG UCCUCUAGUU UUACUAGUCU GUUUACAGG CGUUACACGA UUACUACCUU AGGCGCCUCA AUCUCCU

GENBANK: GENBANK: CP070229.1

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Macromolecule #2: Monomer 1 RT component of the Eco1DRT E.coli defense system.

MacromoleculeName: Monomer 1 RT component of the Eco1DRT E.coli defense system.
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 52.013699 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSSTIFKKH FSTKNLKRIY KDIVSLSPAV GVDNMSHETF WRLQKDEIKT IRRKSLSGDY RFNKYKLKLI SKGRGKAPRE ISIPTIRDK IALRAICDFL QEIYQDVVSF DLPQDMVVSV KEAISEGEYD YFMKFDVANF YPSVVHEQLI KRLRAKIRDE K ILSLISSA ...String:
MSSSTIFKKH FSTKNLKRIY KDIVSLSPAV GVDNMSHETF WRLQKDEIKT IRRKSLSGDY RFNKYKLKLI SKGRGKAPRE ISIPTIRDK IALRAICDFL QEIYQDVVSF DLPQDMVVSV KEAISEGEYD YFMKFDVANF YPSVVHEQLI KRLRAKIRDE K ILSLISSA ISSPTVSKPR RDDLPSNCGV PQGLSISNIL AAIYLLNVDK YYRANKSIKY YRYVDDVMIL CDSTDSEEIT SD LLPRFKR LGLKVYDPKE NPEKSSVGYL HKDDFGYLGY YFQRGIVTAR KGSVENLRES LLSIFTGYKH SKLKSPEFLE WRV NLRVTG CIFQNKSKGW MYFFSEINDE TLLHELDDFL KRLCVRFGVT IKLKSFVRAF FQIKYNRRET SYIPNFDEYD ITKK TYVLT HYFNKSVKGM TDEEIDYHFN KRISKQVKDI ETDVKDAGY

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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 (6k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3000000
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: SGD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 2560000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL / Overall B value: 90
Output model

PDB-30qm:
Cryo-EM structure of the E. coli DRT10 RT-ncRNA complex, Eco1 subtype

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