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- EMDB-63147: Cryo-EM structure of the dGTP bound DRT2-ncRNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63147
TitleCryo-EM structure of the dGTP bound DRT2-ncRNA complex
Map data
Sample
  • Complex: dGTP bound DRT2-ncRNA complex
    • Protein or peptide: RNA-dependent DNA polymerase
    • RNA: RNA (280-MER)
    • DNA: DNA (5'-D(P*GP*AP*TP*AP*T)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
KeywordsANTIVIRAL PROTEIN/RNA/DNA / ANTIVIRAL PROTEIN-RNA-DNA complex
Biological speciesKlebsiella pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsZhang JT / Qing H / Xia YS / Jia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Dual sensing activates antiviral reverse transcriptase for membrane targeting
Authors: Jia N / Zhang JT / Xia YS / Qi H / Song XY
History
DepositionJan 15, 2025-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63147.png

Downloads & links

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Map

FileDownload / File: emd_63147.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 340 pix.
= 281.18 Å		0.83 Å/pix.
x 340 pix.
= 281.18 Å		0.83 Å/pix.
x 340 pix.
= 281.18 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.0017510429 - 2.3321142
Average (Standard dev.)0.00074001565 (±0.02010091)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 281.18 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63147_msk_1.map
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AxesZYX

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Half map: #2

Fileemd_63147_half_map_1.map
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Half map: #1

Fileemd_63147_half_map_2.map
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Sample components

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Entire : dGTP bound DRT2-ncRNA complex

EntireName: dGTP bound DRT2-ncRNA complex
Components
  • Complex: dGTP bound DRT2-ncRNA complex
    • Protein or peptide: RNA-dependent DNA polymerase
    • RNA: RNA (280-MER)
    • DNA: DNA (5'-D(P*GP*AP*TP*AP*T)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: dGTP bound DRT2-ncRNA complex

SupramoleculeName: dGTP bound DRT2-ncRNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Klebsiella pneumoniae (bacteria)

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Macromolecule #1: RNA-dependent DNA polymerase

MacromoleculeName: RNA-dependent DNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 49.788645 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (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 #2: RNA (280-MER)

MacromoleculeName: RNA (280-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 89.970867 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 CUA

GENBANK: GENBANK: CP063277.1

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

MacromoleculeName: DNA (5'-D(P*GP*AP*TP*AP*T)-3') / type: dna / ID: 3 / 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 #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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

MacromoleculeName: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 150565
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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