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- PDB-9ucy: Cryo-EM structure of the R2Tg retrotransposon in complex with R2R... -

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Basic information

Entry
Database: PDB / ID: 9ucy
TitleCryo-EM structure of the R2Tg retrotransposon in complex with R2RNA and rDNA in the initiating target-primed reverse transcription state (top strand cleaved)
Components
  • (28S DNA bottom strand, ...) x 2
  • 28S DNA top strand
  • R2Tg 3'UTR RNA
  • Reverse transcriptase-like protein
KeywordsDNA BINDING PROTEIN / retrotransposon / LINE / reverse transcriptase / endonuclease / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA-DNA complex
Function / homologyTHYMIDINE-5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesTaeniopygia guttata (zebra finch)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsKomatsu, D. / Hiraizumi, M. / Fujimatsu, K. / Yamada, S. / Yamashita, K. / Nishimasu, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and Technology Japan
CitationJournal: To Be Published
Title: Structure mechanism of the avian R2 retrotransposon for programmable gene integration
Authors: Komatsu, D. / Nishimasu, H.
History
DepositionApr 6, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / 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-like protein
B: R2Tg 3'UTR RNA
C: 28S DNA top strand
D: 28S DNA bottom strand, 3' side
E: 28S DNA bottom strand, 5' side (priming strand)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,30912
Polymers233,5175
Non-polymers7927
Water2,810156
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

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28S DNA bottom strand, ... , 2 types, 2 molecules DE

#4: DNA chain 28S DNA bottom strand, 3' side


Mass: 15263.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Taeniopygia guttata (zebra finch)
#5: DNA chain 28S DNA bottom strand, 5' side (priming strand)


Mass: 9550.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Taeniopygia guttata (zebra finch)

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Protein / RNA chain / DNA chain , 3 types, 3 molecules ABC

#1: Protein Reverse transcriptase-like protein


Mass: 146346.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Taeniopygia guttata (zebra finch) / Production host: Spodoptera frugiperda (fall armyworm)
#2: RNA chain R2Tg 3'UTR RNA


Mass: 37589.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Taeniopygia guttata (zebra finch)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#3: DNA chain 28S DNA top strand


Mass: 24766.883 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Taeniopygia guttata (zebra finch) / References: GenBank: 2946502449

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Non-polymers , 4 types, 163 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Details

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: R2Tg-R2RNA-28SDNA ternary complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Taeniopygia guttata (zebra finch)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
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: 800 nm
Image recordingElectron dose: 49.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
9Servalcatmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 472858 / Symmetry type: POINT

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