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- PDB-9lv6: The Cryo-EM Structure of DRT2 -

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Basic information

Entry
Database: PDB / ID: 9lv6
TitleThe Cryo-EM Structure of DRT2
Components
  • Antiviral reverse transcriptase Drt2
  • DNA (5'-D(*GP*AP*TP*AP*T)-3')
  • RNA (281-MER)
KeywordsRNA BINDING PROTEIN/DNA/RNA / DRT2 / ncRNA / reverse transcriptase / RNA BINDING PROTEIN-DNA-RNA complex
Function / homology: / DNA / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsGao, X. / Zhu, H. / Cui, S. / Zhu, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structures of type 2 defense-associated reverse transcriptase (DRT2) systems
Authors: Gao, X. / Zhu, H. / Cui, S. / Zhu, K. / Li, M.
History
DepositionFeb 11, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 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
P: DNA (5'-D(*GP*AP*TP*AP*T)-3')
R: RNA (281-MER)
A: Antiviral reverse transcriptase Drt2
C: DNA (5'-D(*GP*AP*TP*AP*T)-3')
D: RNA (281-MER)
B: Antiviral reverse transcriptase Drt2


Theoretical massNumber of molelcules
Total (without water)283,2166
Polymers283,2166
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: DNA chain DNA (5'-D(*GP*AP*TP*AP*T)-3')


Mass: 1519.048 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: RNA chain RNA (281-MER)


Mass: 90300.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: GenBank: 1920786575
#3: Protein Antiviral reverse transcriptase Drt2


Mass: 49788.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
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: Cryo-EM structure of the DRT2 RT-ncRNA dimer / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 418840 / Symmetry type: POINT
RefinementHighest resolution: 3.55 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00211578
ELECTRON MICROSCOPYf_angle_d0.50516484
ELECTRON MICROSCOPYf_dihedral_angle_d12.1483162
ELECTRON MICROSCOPYf_chiral_restr0.0331950
ELECTRON MICROSCOPYf_plane_restr0.0041400

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