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

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Basic information

Entry
Database: PDB / ID: 30qm
TitleCryo-EM structure of the E. coli DRT10 RT-ncRNA complex, Eco1 subtype
Components
  • Monomer 1 RT component of the Eco1DRT E.coli defense system.
  • ncRNA component of the Eco1DRT10 E.coli defense system.
KeywordsRNA BINDING PROTEIN / phage. defense / RNA
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHe, Q. / Ramirez, J.
Funding support United States, 1items
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, I.S. / Sternberg, S.H.
History
DepositionMay 8, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: ncRNA component of the Eco1DRT10 E.coli defense system.
A: Monomer 1 RT component of the Eco1DRT E.coli defense system.
B: Monomer 1 RT component of the Eco1DRT E.coli defense system.


Theoretical massNumber of molelcules
Total (without water)144,2613
Polymers144,2613
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 40233.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 2173402004
#2: Protein Monomer 1 RT component of the Eco1DRT E.coli defense system.


Mass: 52013.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: E. coli DRT10 RT-ncRNA complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 250 kDa/nm / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 300 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
12RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3000000
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2560000 / Symmetry type: POINT
Atomic model buildingB value: 90 / Protocol: AB INITIO MODEL

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