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- PDB-24nb: DRT4 homohexamer with dGTP, GMP -

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Basic information

Entry
Database: PDB / ID: 24nb
TitleDRT4 homohexamer with dGTP, GMP
ComponentsReverse transcriptase domain-containing protein
KeywordsIMMUNE SYSTEM / DRT4 / reverse transcriptase / terminal transferase / nuclease
Function / homologyReverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / GUANOSINE / Reverse transcriptase domain-containing protein
Function and homology information
Biological speciesEnterobacteriaceae (enterobacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsWang, L. / Li, J.
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
DepositionMar 11, 2026Deposition 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)382,14030
Polymers377,1066
Non-polymers5,03424
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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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
Source: (gene. exp.) Enterobacteriaceae (enterobacteria) / Gene: BZ227_14395 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A628R156
#2: Chemical
ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H13N5O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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 with dGTP, GMP, Mg2+ / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
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
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118142 / Symmetry type: POINT
RefinementHighest resolution: 2.54 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00226262
ELECTRON MICROSCOPYf_angle_d0.58935616
ELECTRON MICROSCOPYf_dihedral_angle_d8.2443713
ELECTRON MICROSCOPYf_chiral_restr0.0393840
ELECTRON MICROSCOPYf_plane_restr0.0044518

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