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- EMDB-63413: The Cryo-EM Structure of DRT2 -

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Basic information

Entry
Database: EMDB / ID: EMD-63413
TitleThe Cryo-EM Structure of DRT2
Map data
Sample
  • Complex: Cryo-EM structure of the DRT2 RT-ncRNA complex
    • DNA: DNA (5'-D(*GP*AP*TP*AP*T)-3')
    • RNA: RNA (281-MER)
    • Protein or peptide: Antiviral reverse transcriptase Drt2
  • Ligand: MAGNESIUM ION
KeywordsDRT2 / ncRNA / reverse transcriptase / RNA BINDING PROTEIN/DNA/RNA / RNA BINDING PROTEIN-DNA-RNA complex
Biological speciesKlebsiella pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsGao X / Zhu H / Cui S / Zhu K
Funding support1 items
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, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63413.png

Downloads & links

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Map

FileDownload / File: emd_63413.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 300 pix.
= 243. Å		0.81 Å/pix.
x 300 pix.
= 243. Å		0.81 Å/pix.
x 300 pix.
= 243. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0017392898 - 1.8094873
Average (Standard dev.)0.00088021543 (±0.020965002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 243.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63413_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63413_half_map_2.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 : Cryo-EM structure of the DRT2 RT-ncRNA complex

EntireName: Cryo-EM structure of the DRT2 RT-ncRNA complex
Components
  • Complex: Cryo-EM structure of the DRT2 RT-ncRNA complex
    • DNA: DNA (5'-D(*GP*AP*TP*AP*T)-3')
    • RNA: RNA (281-MER)
    • Protein or peptide: Antiviral reverse transcriptase Drt2
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Cryo-EM structure of the DRT2 RT-ncRNA complex

SupramoleculeName: Cryo-EM structure of the DRT2 RT-ncRNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Klebsiella pneumoniae (bacteria)

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Macromolecule #1: DNA (5'-D(*GP*AP*TP*AP*T)-3')

MacromoleculeName: DNA (5'-D(*GP*AP*TP*AP*T)-3') / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 1.519048 KDa
SequenceString:
(DG)(DA)(DT)(DA)(DT)

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Macromolecule #2: RNA (281-MER)

MacromoleculeName: RNA (281-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 90.30007 KDa
SequenceString: GCCCUAAACA AAGGUUUAGG GGUAUUGUAC AGGUUGUCAA GCCUCCCACA GGUCUUGGUG AAACCAAUCA CUGUGACGAC GGUAAGCAA CACUUGGAUG AUAUUCAUAA UUGACUCCAC GCUACUGAUU ACAUUAUACA GCAUAUCUAA CAUUUGCGGC G AGGUUCAC ...String:
GCCCUAAACA AAGGUUUAGG GGUAUUGUAC AGGUUGUCAA GCCUCCCACA GGUCUUGGUG AAACCAAUCA CUGUGACGAC GGUAAGCAA CACUUGGAUG AUAUUCAUAA UUGACUCCAC GCUACUGAUU ACAUUAUACA GCAUAUCUAA CAUUUGCGGC G AGGUUCAC AAUUUGUAUU UAGGUACUGA UUGUGGAUGA GAAGGUUGGA GAAAGACCAC UUGGUUAAGC CGGAGGAUGU GU CCUAGAA UUGUCGCUAU UCUGUCAUCC UCCGGUUUUG CUAA

GENBANK: GENBANK: CP063277.1

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Macromolecule #3: Antiviral reverse transcriptase Drt2

MacromoleculeName: Antiviral reverse transcriptase Drt2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 49.788645 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNNDDYPWFR KRGYLHFDEP VSLKKAVKYV SSPEKIIKHS FLPFLSFEVK SFKIKKDKST KQLSKTEKLR PIAYSSHLDS HIYAFYAEY LTGHYELLIQ ENNLHENILA FRSLNKSNIE FAKRAFDTIT EMGECSAVAL DLSGFFDNLD HQILKHQWCK V IGTEALPQ ...String:
MNNDDYPWFR KRGYLHFDEP VSLKKAVKYV SSPEKIIKHS FLPFLSFEVK SFKIKKDKST KQLSKTEKLR PIAYSSHLDS HIYAFYAEY LTGHYELLIQ ENNLHENILA FRSLNKSNIE FAKRAFDTIT EMGECSAVAL DLSGFFDNLD HQILKHQWCK V IGTEALPQ DHFAIYKSIT RYSKVDKNRA YEILGISKNN PKYNRRKICT PVDFRNKIRK NGLIIVNNSQ KGIPQGSPIS AL LSNIYML DFDIEMRDYA QERGGHYYRY CDDMLFIVPT KYNKTLAGDV AQRIKHLKVE LNTKKTEIRD FIYKDSTLVA NMP LQYLGF IFDGSNILLR SSSLARYSER MKRGVRLAKA TMDSKNRIRE NKGEALKALF KKKLYARYSH IGRRNFLTYG YRAA KIMNS KAIKRQLKPL QKRLENEILK

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9c0i

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103560
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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