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- EMDB-69684: DRT4 homohexamer with dGTP, ssRNA (local refinement) -

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Basic information

Entry
Database: EMDB / ID: EMD-69684
TitleDRT4 homohexamer with dGTP, ssRNA (local refinement)
Map data
Sample
  • Complex: DRT4 homohexamer with dGTP, ssRNA, Mg2+
    • Protein or peptide: Reverse transcriptase domain-containing protein
    • RNA: RNA (5'-R(P*UP*UP*GP*U)-3')
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsDRT4 / reverse transcriptase / terminal transferase / nuclease / IMMUNE SYSTEM
Function / homologyReverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase domain-containing protein
Function and homology information
Biological speciesEnterobacteriaceae (enterobacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsWang L / Li J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Science / Year: 2026
Title: DNA polymerization activates RNA cleavage of a reverse transcriptase-like antiviral enzyme
Authors: Rong X / Xiao J / Zhao X / Yan Y / Li J / Chen Y / Fan Y / Liu Z / Cao Y / Chen F / Cheng R / Wang X / Wang L / Zhu B
History
DepositionMar 11, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_69684.png

Downloads & links

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Map

FileDownload / File: emd_69684.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 316.416 Å		0.82 Å/pix.
x 384 pix.
= 316.416 Å		0.82 Å/pix.
x 384 pix.
= 316.416 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.157
Minimum - Maximum-0.83712447 - 1.4642098
Average (Standard dev.)-0.0002652622 (±0.043213308)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 316.41602 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_69684_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_69684_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 : DRT4 homohexamer with dGTP, ssRNA, Mg2+

EntireName: DRT4 homohexamer with dGTP, ssRNA, Mg2+
Components
  • Complex: DRT4 homohexamer with dGTP, ssRNA, Mg2+
    • Protein or peptide: Reverse transcriptase domain-containing protein
    • RNA: RNA (5'-R(P*UP*UP*GP*U)-3')
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: DRT4 homohexamer with dGTP, ssRNA, Mg2+

SupramoleculeName: DRT4 homohexamer with dGTP, ssRNA, Mg2+ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Enterobacteriaceae (enterobacteria)

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Macromolecule #1: Reverse transcriptase domain-containing protein

MacromoleculeName: Reverse transcriptase domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteriaceae (enterobacteria)
Molecular weightTheoretical: 62.850957 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVIFDEKRHL YEALLRHNYF PNQKGSISEI PPCFSSRTFT PEIAELISSD TSGRRSLQGY DCVEYYATRY NNFPRTLSII HPKAYSKLA KHIHDNWEEI RFIKENENSM IKPDMHADGR IIIMNYEDAE TKTIRELNDG FGRRFKVNAD ISGCFTNIYS H SIPWAVIG ...String:
MVIFDEKRHL YEALLRHNYF PNQKGSISEI PPCFSSRTFT PEIAELISSD TSGRRSLQGY DCVEYYATRY NNFPRTLSII HPKAYSKLA KHIHDNWEEI RFIKENENSM IKPDMHADGR IIIMNYEDAE TKTIRELNDG FGRRFKVNAD ISGCFTNIYS H SIPWAVIG VNNAKIALNT KVKNQDKHWS DKLDYFQRQA KRNETHGVPI GPATSSIVCE IILSAVDKRL RDDGFLFRRY ID DYTCYCK THDDAKEFLH LLGMELSKYK LSLNLHKTKI TNLPGTLNDN WVSLLNVNSP TKKRFTDQDL NKLSSSEVIN FLD YAVQLN TQVGGGSILK YAISLVINNL DEYTITQVYD YLLNLSWHYP MLIPYLGVLI EHVYLDDGDE YKNKFNEILS MCAE NKCSD GMAWTLYFCI KNNIDIDDDV IEKIICFGDC LSLCLLDSSD IYEEKINNFV SDIIKLDYEY DIDRYWLLFY QRFFK DKAP SPYNDKCFDI MKGYGVDFMP DENYKTKAES YCHVVNNPFL EDGDEIVSFN DYMAIA

UniProtKB: Reverse transcriptase domain-containing protein

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Macromolecule #2: RNA (5'-R(P*UP*UP*GP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*GP*U)-3') / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.05574 KDa
SequenceString:
UUUGUUUUUU

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Macromolecule #3: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: DGT
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-DGT:
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 12 / 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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

21ou

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 132315
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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