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- PDB-9vdo: Cryo-EM structure of the substrate bound DRT4 -

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Basic information

Entry
Database: PDB / ID: 9vdo
TitleCryo-EM structure of the substrate bound DRT4
Components
  • DNA (5'-D(P*CP*CP*CP*AP*A)-3')
  • Reverse transcriptase domain-containing protein
KeywordsDNA BINDING PROTEIN/DNA / UG15 / DRT4 / Reverse transcriptases / UG/Abi system / DNA BINDING PROTEIN-DNA complex
Function / homologyReverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / : / DNA / Reverse transcriptase domain-containing protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsWang, Y. / Deng, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the substrate bound DRT4
Authors: Wang, Y. / Deng, Z.
History
DepositionJun 9, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data 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
I: DNA (5'-D(P*CP*CP*CP*AP*A)-3')
B: Reverse transcriptase domain-containing protein
C: DNA (5'-D(P*CP*CP*CP*AP*A)-3')
D: Reverse transcriptase domain-containing protein
E: DNA (5'-D(P*CP*CP*CP*AP*A)-3')
F: Reverse transcriptase domain-containing protein
G: DNA (5'-D(P*CP*CP*CP*AP*A)-3')
H: Reverse transcriptase domain-containing protein
J: DNA (5'-D(P*CP*CP*CP*AP*A)-3')
K: Reverse transcriptase domain-containing protein
L: DNA (5'-D(P*CP*CP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)395,62230
Polymers392,16012
Non-polymers3,46218
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: 63911.047 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BZ227_14395 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A628R156
#2: DNA chain
DNA (5'-D(P*CP*CP*CP*AP*A)-3')


Mass: 1449.002 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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-DNA-dNTP / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
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

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
8PHENIXmodel refinement
13Coot3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 277716 / Symmetry type: POINT
RefinementHighest resolution: 2.93 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00425662
ELECTRON MICROSCOPYf_angle_d0.77734872
ELECTRON MICROSCOPYf_dihedral_angle_d15.0943558
ELECTRON MICROSCOPYf_chiral_restr0.0513762
ELECTRON MICROSCOPYf_plane_restr0.0074350

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