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

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Basic information

Entry
Database: PDB / ID: 9ucz
TitleCryo-EM structure of the R2Tg retrotransposon in complex with R2RNA and rDNA in the initiating target-primed reverse transcription state (ZF3/2 disordered)
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: 2.61 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

Downloads & links

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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
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

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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 , 3 types, 7 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

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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
4cryoSPARCCTF correction
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13Servalcatmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 441626 / Symmetry type: POINT
RefinementResolution: 2.61→2.61 Å / Num. reflection obs: 2838426 / Average fsc work: 0.8018
Displacement parametersBiso mean: 41 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.0054127700.0115
ELECTRON MICROSCOPYs_angle_nonh_deg1.3853181251.8299
ELECTRON MICROSCOPYs_dihedral_angle_1_deg5.6310075
ELECTRON MICROSCOPYs_dihedral_angle_2_deg3.42774305
ELECTRON MICROSCOPYs_dihedral_angle_3_deg11.2249222210
ELECTRON MICROSCOPYs_dihedral_angle_6_deg14.766942210
ELECTRON MICROSCOPYs_chiral_restr0.051320690.1226
ELECTRON MICROSCOPYs_planes0.0055146170.02
ELECTRON MICROSCOPYs_nbd0.1873140390.2
ELECTRON MICROSCOPYs_nbtor0.2065178430.2
ELECTRON MICROSCOPYs_hbond_nbd0.14152990.2
ELECTRON MICROSCOPYs_metal_ion0.1616140.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
2.7-2.729ELECTRON MICROSCOPY878370.5075
2.729-2.754ELECTRON MICROSCOPY753250.5336
2.754-2.779ELECTRON MICROSCOPY731550.5592
2.78-2.805ELECTRON MICROSCOPY717970.584
2.806-2.832ELECTRON MICROSCOPY702970.6096
2.832-2.859ELECTRON MICROSCOPY702690.6361
2.859-2.887ELECTRON MICROSCOPY669430.6591
2.887-2.915ELECTRON MICROSCOPY668610.6818
2.915-2.944ELECTRON MICROSCOPY654970.6999
2.944-2.973ELECTRON MICROSCOPY640950.719
2.973-3.003ELECTRON MICROSCOPY629050.7397
3.003-3.033ELECTRON MICROSCOPY610450.7608
3.034-3.064ELECTRON MICROSCOPY611490.7781
3.065-3.096ELECTRON MICROSCOPY593830.7956
3.096-3.129ELECTRON MICROSCOPY579450.8131
3.129-3.162ELECTRON MICROSCOPY561610.8333
3.162-3.195ELECTRON MICROSCOPY553630.8518
3.196-3.23ELECTRON MICROSCOPY542730.8677
3.23-3.265ELECTRON MICROSCOPY531730.8811
3.266-3.301ELECTRON MICROSCOPY518850.8888
3.302-3.338ELECTRON MICROSCOPY512950.8912
3.339-3.376ELECTRON MICROSCOPY498450.8886
3.376-3.415ELECTRON MICROSCOPY486370.8862
3.415-3.454ELECTRON MICROSCOPY472390.8862
3.454-3.494ELECTRON MICROSCOPY465690.8877
3.495-3.536ELECTRON MICROSCOPY457690.8912
3.536-3.578ELECTRON MICROSCOPY440670.8935
3.579-3.621ELECTRON MICROSCOPY432730.8917
3.622-3.666ELECTRON MICROSCOPY423330.8883
3.666-3.712ELECTRON MICROSCOPY415930.886
3.712-3.758ELECTRON MICROSCOPY400150.8889
3.759-3.806ELECTRON MICROSCOPY391890.8932
3.806-3.855ELECTRON MICROSCOPY378610.8952
3.856-3.906ELECTRON MICROSCOPY374550.8949
3.906-3.957ELECTRON MICROSCOPY363730.8937
3.958-4.01ELECTRON MICROSCOPY350130.8944
4.011-4.065ELECTRON MICROSCOPY348490.897
4.065-4.121ELECTRON MICROSCOPY333430.8991
4.121-4.179ELECTRON MICROSCOPY328650.8994
4.179-4.238ELECTRON MICROSCOPY312850.8997
4.238-4.299ELECTRON MICROSCOPY306030.9012
4.299-4.362ELECTRON MICROSCOPY303130.9012
4.362-4.426ELECTRON MICROSCOPY287410.902
4.427-4.492ELECTRON MICROSCOPY284550.9035
4.493-4.561ELECTRON MICROSCOPY271570.9038
4.562-4.632ELECTRON MICROSCOPY270450.9024
4.633-4.705ELECTRON MICROSCOPY257770.8973
4.707-4.78ELECTRON MICROSCOPY244350.8906
4.781-4.857ELECTRON MICROSCOPY242770.8864
4.859-4.938ELECTRON MICROSCOPY233170.8851
4.939-5.021ELECTRON MICROSCOPY228510.8832
5.022-5.106ELECTRON MICROSCOPY217450.878
5.108-5.196ELECTRON MICROSCOPY210330.8725
5.197-5.288ELECTRON MICROSCOPY207130.8636
5.289-5.383ELECTRON MICROSCOPY196470.857
5.384-5.482ELECTRON MICROSCOPY188410.8502
5.483-5.583ELECTRON MICROSCOPY182170.8446
5.585-5.691ELECTRON MICROSCOPY177270.8391
5.692-5.801ELECTRON MICROSCOPY171250.8371
5.803-5.915ELECTRON MICROSCOPY161250.8396
5.917-6.035ELECTRON MICROSCOPY158710.8402
6.037-6.16ELECTRON MICROSCOPY152250.8404
6.161-6.289ELECTRON MICROSCOPY145330.8389
6.291-6.425ELECTRON MICROSCOPY137530.8356
6.426-6.564ELECTRON MICROSCOPY130590.8265
6.567-6.713ELECTRON MICROSCOPY129730.8232
6.717-6.868ELECTRON MICROSCOPY120210.8171
6.869-7.027ELECTRON MICROSCOPY117310.8202
7.031-7.198ELECTRON MICROSCOPY109810.8237
7.201-7.376ELECTRON MICROSCOPY107250.8346
7.378-7.563ELECTRON MICROSCOPY101170.8467
7.565-7.759ELECTRON MICROSCOPY93750.8553
7.762-7.963ELECTRON MICROSCOPY91330.858
7.969-8.184ELECTRON MICROSCOPY85770.8561
8.187-8.414ELECTRON MICROSCOPY82270.8495
8.418-8.655ELECTRON MICROSCOPY75970.8521
8.662-8.916ELECTRON MICROSCOPY73770.8658
8.92-9.191ELECTRON MICROSCOPY69010.879
9.195-9.482ELECTRON MICROSCOPY63030.885
9.487-9.793ELECTRON MICROSCOPY60730.8804
9.798-10.119ELECTRON MICROSCOPY56130.8797
10.13-10.479ELECTRON MICROSCOPY52750.8862
10.486-10.86ELECTRON MICROSCOPY49810.8948
10.867-11.261ELECTRON MICROSCOPY45330.8945
11.277-11.711ELECTRON MICROSCOPY43030.8951
11.72-12.188ELECTRON MICROSCOPY40170.9065
12.198-12.706ELECTRON MICROSCOPY35650.9103
12.718-13.27ELECTRON MICROSCOPY33010.9094
13.283-13.871ELECTRON MICROSCOPY29910.9103
13.901-14.563ELECTRON MICROSCOPY28570.9098
14.58-15.308ELECTRON MICROSCOPY25170.9088
15.348-16.11ELECTRON MICROSCOPY21790.9129
16.157-17.053ELECTRON MICROSCOPY20850.9127
17.081-18.084ELECTRON MICROSCOPY18610.9217
18.117-19.247ELECTRON MICROSCOPY16690.933
19.368-20.57ELECTRON MICROSCOPY13110.9289
20.619-22.028ELECTRON MICROSCOPY12490.9191
22.149-23.847ELECTRON MICROSCOPY10890.9019
24-25.909ELECTRON MICROSCOPY9070.8809
26.007-28.109ELECTRON MICROSCOPY7290.8663
28.489-31.323ELECTRON MICROSCOPY6250.8798
31.496-34.972ELECTRON MICROSCOPY5710.881
35.214-39.577ELECTRON MICROSCOPY3810.8819
39.929-45.567ELECTRON MICROSCOPY3010.9014
46.106-52.821ELECTRON MICROSCOPY2250.9242
54.553-65.204ELECTRON MICROSCOPY1750.932
66.814-82.872ELECTRON MICROSCOPY1050.9484
86.256-105.642ELECTRON MICROSCOPY490.9822
121.985-298.8ELECTRON MICROSCOPY400.9176

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