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- PDB-9ud0: Cryo-EM structure of R2Tg bound to template RNA and target DNA in... -

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Basic information

Entry
Database: PDB / ID: 9ud0
TitleCryo-EM structure of R2Tg bound to template RNA and target DNA in the target-primed reverse transcription initiation state (state 1, Myb domain focused)
Components
  • 28S DNA bottom strand, 3' side
  • 28S DNA top strand
  • Reverse transcriptase-like protein
KeywordsDNA BINDING PROTEIN / retrotransposon / LINE / reverse transcriptase / endonuclease / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA-DNA complex
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesTaeniopygia guttata (zebra finch)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 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
C: 28S DNA top strand
D: 28S DNA bottom strand, 3' side


Theoretical massNumber of molelcules
Total (without water)186,3773
Polymers186,3773
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-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: 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
#3: 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)
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: all / 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: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168252 / Symmetry type: POINT
RefinementResolution: 3.14→3.14 Å / Num. reflection obs: 2838426 / Average fsc work: 0.6322
Displacement parametersBiso mean: 187.23 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.006116350.0112
ELECTRON MICROSCOPYs_angle_nonh_deg1.776623981.8255
ELECTRON MICROSCOPYs_dihedral_angle_1_deg5.28673624.1436
ELECTRON MICROSCOPYs_dihedral_angle_2_deg2.9992685
ELECTRON MICROSCOPYs_dihedral_angle_3_deg12.920517210
ELECTRON MICROSCOPYs_dihedral_angle_6_deg15.37133210
ELECTRON MICROSCOPYs_chiral_restr0.15673150.1713
ELECTRON MICROSCOPYs_planes0.005215530.02
ELECTRON MICROSCOPYs_nbd0.199716160.2
ELECTRON MICROSCOPYs_nbtor0.209218870.2
ELECTRON MICROSCOPYs_hbond_nbd0.1838370.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
2.7-2.729ELECTRON MICROSCOPY878370.1532
2.729-2.754ELECTRON MICROSCOPY753250.1736
2.754-2.779ELECTRON MICROSCOPY731550.1762
2.78-2.805ELECTRON MICROSCOPY717970.1749
2.806-2.832ELECTRON MICROSCOPY702970.1891
2.832-2.859ELECTRON MICROSCOPY702690.22
2.859-2.887ELECTRON MICROSCOPY669430.269
2.887-2.915ELECTRON MICROSCOPY668610.3181
2.915-2.944ELECTRON MICROSCOPY654970.3564
2.944-2.973ELECTRON MICROSCOPY640950.388
2.973-3.003ELECTRON MICROSCOPY629050.4197
3.003-3.033ELECTRON MICROSCOPY610450.4519
3.034-3.064ELECTRON MICROSCOPY611490.488
3.065-3.096ELECTRON MICROSCOPY593830.5385
3.096-3.129ELECTRON MICROSCOPY579450.6008
3.129-3.162ELECTRON MICROSCOPY561610.6701
3.162-3.195ELECTRON MICROSCOPY553630.7323
3.196-3.23ELECTRON MICROSCOPY542730.7869
3.23-3.265ELECTRON MICROSCOPY531730.8232
3.266-3.301ELECTRON MICROSCOPY518850.8419
3.302-3.338ELECTRON MICROSCOPY512950.8451
3.339-3.376ELECTRON MICROSCOPY498450.8385
3.376-3.415ELECTRON MICROSCOPY486370.8309
3.415-3.454ELECTRON MICROSCOPY472390.8247
3.454-3.494ELECTRON MICROSCOPY465690.824
3.495-3.536ELECTRON MICROSCOPY457690.8272
3.536-3.578ELECTRON MICROSCOPY440670.827
3.579-3.621ELECTRON MICROSCOPY432730.8222
3.622-3.666ELECTRON MICROSCOPY423330.8122
3.666-3.712ELECTRON MICROSCOPY415930.804
3.712-3.758ELECTRON MICROSCOPY400150.7986
3.759-3.806ELECTRON MICROSCOPY391890.7961
3.806-3.855ELECTRON MICROSCOPY378610.8004
3.856-3.906ELECTRON MICROSCOPY374550.8078
3.906-3.957ELECTRON MICROSCOPY363730.8165
3.958-4.01ELECTRON MICROSCOPY350130.8226
4.011-4.065ELECTRON MICROSCOPY348490.8272
4.065-4.121ELECTRON MICROSCOPY333430.828
4.121-4.179ELECTRON MICROSCOPY328650.8289
4.179-4.238ELECTRON MICROSCOPY312850.8269
4.238-4.299ELECTRON MICROSCOPY306030.8244
4.299-4.362ELECTRON MICROSCOPY303130.8209
4.362-4.426ELECTRON MICROSCOPY287410.8187
4.427-4.492ELECTRON MICROSCOPY284550.8157
4.493-4.561ELECTRON MICROSCOPY271570.8126
4.562-4.632ELECTRON MICROSCOPY270450.8066
4.633-4.705ELECTRON MICROSCOPY257770.7998
4.707-4.78ELECTRON MICROSCOPY244350.7917
4.781-4.857ELECTRON MICROSCOPY242770.7853
4.859-4.938ELECTRON MICROSCOPY233170.7826
4.939-5.021ELECTRON MICROSCOPY228510.7805
5.022-5.106ELECTRON MICROSCOPY217450.781
5.108-5.196ELECTRON MICROSCOPY210330.7821
5.197-5.288ELECTRON MICROSCOPY207130.786
5.289-5.383ELECTRON MICROSCOPY196470.7911
5.384-5.482ELECTRON MICROSCOPY188410.7927
5.483-5.583ELECTRON MICROSCOPY182170.792
5.585-5.691ELECTRON MICROSCOPY177270.7886
5.692-5.801ELECTRON MICROSCOPY171250.7839
5.803-5.915ELECTRON MICROSCOPY161250.7778
5.917-6.035ELECTRON MICROSCOPY158710.7731
6.037-6.16ELECTRON MICROSCOPY152250.7697
6.161-6.289ELECTRON MICROSCOPY145330.7634
6.291-6.425ELECTRON MICROSCOPY137530.7604
6.426-6.564ELECTRON MICROSCOPY130590.7546
6.567-6.713ELECTRON MICROSCOPY129730.7539
6.717-6.868ELECTRON MICROSCOPY120210.7527
6.869-7.027ELECTRON MICROSCOPY117310.7579
7.031-7.198ELECTRON MICROSCOPY109810.7715
7.201-7.376ELECTRON MICROSCOPY107250.7874
7.378-7.563ELECTRON MICROSCOPY101170.8042
7.565-7.759ELECTRON MICROSCOPY93750.8262
7.762-7.963ELECTRON MICROSCOPY91330.8481
7.969-8.184ELECTRON MICROSCOPY85770.8692
8.187-8.414ELECTRON MICROSCOPY82270.8854
8.418-8.655ELECTRON MICROSCOPY75970.8946
8.662-8.916ELECTRON MICROSCOPY73770.8996
8.92-9.191ELECTRON MICROSCOPY69010.9013
9.195-9.482ELECTRON MICROSCOPY63030.9026
9.487-9.793ELECTRON MICROSCOPY60730.9026
9.798-10.119ELECTRON MICROSCOPY56130.9056
10.13-10.479ELECTRON MICROSCOPY52750.9123
10.486-10.86ELECTRON MICROSCOPY49810.9192
10.867-11.261ELECTRON MICROSCOPY45330.927
11.277-11.711ELECTRON MICROSCOPY43030.9351
11.72-12.188ELECTRON MICROSCOPY40170.9403
12.198-12.706ELECTRON MICROSCOPY35650.9435
12.718-13.27ELECTRON MICROSCOPY33010.9418
13.283-13.871ELECTRON MICROSCOPY29910.9381
13.901-14.563ELECTRON MICROSCOPY28570.9331
14.58-15.308ELECTRON MICROSCOPY25170.9296
15.348-16.11ELECTRON MICROSCOPY21790.9303
16.157-17.053ELECTRON MICROSCOPY20850.9311
17.081-18.084ELECTRON MICROSCOPY18610.9335
18.117-19.247ELECTRON MICROSCOPY16690.9333
19.368-20.57ELECTRON MICROSCOPY13110.9319
20.619-22.028ELECTRON MICROSCOPY12490.9298
22.149-23.847ELECTRON MICROSCOPY10890.9239
24-25.909ELECTRON MICROSCOPY9070.9115
26.007-28.109ELECTRON MICROSCOPY7290.9059
28.489-31.323ELECTRON MICROSCOPY6250.9099
31.496-34.972ELECTRON MICROSCOPY5710.9174
35.214-39.577ELECTRON MICROSCOPY3810.9351
39.929-45.567ELECTRON MICROSCOPY3010.9471
46.106-52.821ELECTRON MICROSCOPY2250.9581
54.553-65.204ELECTRON MICROSCOPY1750.9672
66.814-82.872ELECTRON MICROSCOPY1050.9743
86.256-105.642ELECTRON MICROSCOPY490.9799
121.985-298.8ELECTRON MICROSCOPY400.8748

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