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- PDB-21ou: DRT4 homohexamer -

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Basic information

Entry
Database: PDB / ID: 21ou
TitleDRT4 homohexamer
Components
  • DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • Reverse transcriptase domain-containing protein
KeywordsRNA BINDING PROTEIN/DNA / DRT4 / reverse transcriptase / terminal transferase / nuclease / RNA BINDING PROTEIN-DNA complex
Function / homologyReverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / DNA / Reverse transcriptase domain-containing protein
Function and homology information
Biological speciesEnterobacteriaceae (enterobacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.34 Å
AuthorsXiao, J. / Wang, L.
Funding support1items
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
DepositionDec 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reverse transcriptase domain-containing protein
B: Reverse transcriptase domain-containing protein
C: Reverse transcriptase domain-containing protein
D: Reverse transcriptase domain-containing protein
E: Reverse transcriptase domain-containing protein
F: Reverse transcriptase domain-containing protein
G: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
H: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
I: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
J: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
K: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
L: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)391,87012
Polymers391,87012
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: Protein
Reverse transcriptase domain-containing protein


Mass: 62850.957 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Sequence reference for strain 'Enterobacteriaceae' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A628R156.
Source: (gene. exp.) Enterobacteriaceae (enterobacteria) / Gene: BZ227_14395 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A628R156
#2: DNA chain
DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2460.697 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteriaceae (enterobacteria) / 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: DRT4 homohexamer / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Enterobacteriaceae (enterobacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
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: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 217690 / Symmetry type: POINT
RefinementHighest resolution: 2.34 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00227078
ELECTRON MICROSCOPYf_angle_d0.38436858
ELECTRON MICROSCOPYf_dihedral_angle_d14.3924062
ELECTRON MICROSCOPYf_chiral_restr0.0363972
ELECTRON MICROSCOPYf_plane_restr0.0034554

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