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- EMDB-64056: Cryo-EM structure of R2Tg bound to template RNA and target DNA in... -

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Basic information

Entry
Database: EMDB / ID: EMD-64056
TitleCryo-EM structure of R2Tg bound to template RNA and target DNA in the target-primed reverse transcription initiation state (state 3)
Map data
Sample
  • Complex: R2Tg-R2RNA-28SDNA ternary complex
    • Protein or peptide: Reverse transcriptase-like protein
    • RNA: R2Tg 3'UTR RNA
    • DNA: 28S DNA top strand
    • DNA: 28S DNA bottom strand, 3' side
    • DNA: 28S DNA bottom strand, 5' side (priming strand)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE
Keywordsretrotransposon / LINE / reverse transcriptase / endonuclease / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA-DNA complex / DNA BINDING PROTEIN
Biological speciesTaeniopygia guttata (zebra finch)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsKomatsu D / Hiraizumi M / Fujimatsu K / Yamada S / Yamashita K / Nishimasu H
Funding support Japan, 1 items
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, 2025-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64056.png

Downloads & links

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Map

FileDownload / File: emd_64056.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 300 pix.
= 298.8 Å		1 Å/pix.
x 300 pix.
= 298.8 Å		1 Å/pix.
x 300 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.996 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.10526116 - 0.3088151
Average (Standard dev.)-0.000248882 (±0.006058535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64056_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64056_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64056_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : R2Tg-R2RNA-28SDNA ternary complex

EntireName: R2Tg-R2RNA-28SDNA ternary complex
Components
  • Complex: R2Tg-R2RNA-28SDNA ternary complex
    • Protein or peptide: Reverse transcriptase-like protein
    • RNA: R2Tg 3'UTR RNA
    • DNA: 28S DNA top strand
    • DNA: 28S DNA bottom strand, 3' side
    • DNA: 28S DNA bottom strand, 5' side (priming strand)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE

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Supramolecule #1: R2Tg-R2RNA-28SDNA ternary complex

SupramoleculeName: R2Tg-R2RNA-28SDNA ternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Taeniopygia guttata (zebra finch)

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Macromolecule #1: Reverse transcriptase-like protein

MacromoleculeName: Reverse transcriptase-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Taeniopygia guttata (zebra finch)
Molecular weightTheoretical: 146.346734 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSYYHHHHHH DGASWSHPQF EKGGGSGGGS GGSAWSHPQF EKGGSTTLEV LFQGPELFVP EEGSSEKESE DAPKTSPPTP GKHGLEQTG EEKVMVTVPD KNPPCPCCGT RVNSVLNLIE HLKVSHGKRG VCFRCAKCGK ENSNYHSVVC HFPKCRGPET E KAPAGEWI ...String:
MSYYHHHHHH DGASWSHPQF EKGGGSGGGS GGSAWSHPQF EKGGSTTLEV LFQGPELFVP EEGSSEKESE DAPKTSPPTP GKHGLEQTG EEKVMVTVPD KNPPCPCCGT RVNSVLNLIE HLKVSHGKRG VCFRCAKCGK ENSNYHSVVC HFPKCRGPET E KAPAGEWI CEVCNRDFTT KIGLGQHKRL AHPAVRNQER IVASQPKETS NRGAHKRCWT KEEEELLIRL EAQFEGNKNI NK LIAEHIT TKTAKQISDK RRLLSRKPAE EPREEPGTCH HTRRAAASLR TEPEMSHHAQ AEDRDNGPGR RPLPGRAAAG GRT MDEIRR HPDKGNGQQR PTKQKSEEQL QAYYKKTLEE RLSAGALNTF PRAFKQVMEG RDIKLVINQT AQDCFGCLES ISQI RTATR DKKDTVTREK HPKKPFQKWM KDRAIKKGNY LRFQRLFYLD RGKLAKIILD DIECLSCDIP LSEIYSVFKT RWETT GSFK SLGDFKTYGK ADNTAFRELI TAKEIEKNVQ EMSKGSAPGP DGITLGDVVK MDPEFSRTME IFNLWLTTGK IPDMVR GCR TVLIPKSSKP DRLKDINNWR PITIGSILLR LFSRIVTARL SKACPLNPRQ RGFIRAAGCS ENLKLLQTII WSAKREH RP LGVVFVDIAK AFDTVSHQHI IHALQQREVD PHIVGLVSNM YENISTYITT KRNTHTDKIQ IRVGVKQGDP MSPLLFNL A MDPLLCKLEE SGKGYHRGQS SITAMAFADD LVLLSDSWEN MNTNISILET FCNLTGLKTQ GQKCHGFYIK PTKDSYTIN DCAAWTINGT PLNMIDPGES EKYLGLQFDP WIGIARSGLS TKLDFWLQRI DQAPLKPLQK TDILKTYTIP RLIYIADHSE VKTALLETL DQKIRTAVKE WLHLPPCTCD AILYSSTRDG GLGITKLAGL IPSVQARRLH RIAQSSDDTM KCFMEKEKME Q LHKKLWIQ AGGDRENIPS IWEAPPSSEP PNNVSTNSEW EAPTQKDKFP KPCNWRKNEF KKWTKLASQG RGIVNFERDK IS NHWIQYY RRIPHRKLLT ALQLRANVYP TREFLARGRQ DQYIKACRHC DADIESCAHI IGNCPVTQDA RIKRHNYICE LLL EEAKKK DWVVFKEPHI RDSNKELYKP DLIFVKDARA LVVDVTVRYE AAKSSLEEAA AEKVRKYKHL ETEVRHLTNA KDVT FVGFP LGARGKWHQD NFKLLTELGL SKSRQVKMAE TFSTVALFSS VDIVHMFASR ARKSMVMGGS DYKDHDGDYK DHDID YKDD DDK

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Macromolecule #2: R2Tg 3'UTR RNA

MacromoleculeName: R2Tg 3'UTR RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Taeniopygia guttata (zebra finch)
Molecular weightTheoretical: 37.589289 KDa
SequenceString:
GGCACCUGAU UUGGACCAAU UCACGGGAUU UGUCCAAGGU GGACGGGCCA CCUUUACUUA ACCCGGAAAA GGAACAUAUA UAAUUUAUG UGUGUUCGAU AAAUAGCCAA AUGCCUCG

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Macromolecule #3: 28S DNA top strand

MacromoleculeName: 28S DNA top strand / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Taeniopygia guttata (zebra finch)
Molecular weightTheoretical: 24.766883 KDa
SequenceString: (DA)(DT)(DT)(DC)(DA)(DA)(DT)(DG)(DA)(DA) (DG)(DC)(DG)(DC)(DG)(DG)(DG)(DT)(DA)(DA) (DA)(DC)(DG)(DG)(DC)(DG)(DG)(DG)(DA) (DG)(DT)(DA)(DA)(DC)(DT)(DA)(DT)(DG)(DA) (DC) (DT)(DC)(DT)(DC)(DT)(DT) ...String:
(DA)(DT)(DT)(DC)(DA)(DA)(DT)(DG)(DA)(DA) (DG)(DC)(DG)(DC)(DG)(DG)(DG)(DT)(DA)(DA) (DA)(DC)(DG)(DG)(DC)(DG)(DG)(DG)(DA) (DG)(DT)(DA)(DA)(DC)(DT)(DA)(DT)(DG)(DA) (DC) (DT)(DC)(DT)(DC)(DT)(DT)(DA)(DA) (DG)(DG)(DT)(DA)(DG)(DC)(DC)(DA)(DA)(DA) (DT)(DG) (DC)(DC)(DT)(DC)(DG)(DT)(DC) (DA)(DT)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG) (DT)(DG)(DA)

GENBANK: GENBANK: XR_011979195.1

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

MacromoleculeName: 28S DNA bottom strand, 3' side / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Taeniopygia guttata (zebra finch)
Molecular weightTheoretical: 15.263787 KDa
SequenceString:
(DC)(DC)(DT)(DT)(DA)(DA)(DG)(DA)(DG)(DA) (DG)(DT)(DC)(DA)(DT)(DA)(DG)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DG)(DC)(DC)(DG) (DT)(DT)(DT)(DA)(DC)(DC)(DC)(DG)(DC)(DG) (DC) (DT)(DT)(DC)(DA)(DT)(DT)(DG)(DA) (DA)(DT)

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Macromolecule #5: 28S DNA bottom strand, 5' side (priming strand)

MacromoleculeName: 28S DNA bottom strand, 5' side (priming strand) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Taeniopygia guttata (zebra finch)
Molecular weightTheoretical: 9.550182 KDa
SequenceString:
(DT)(DC)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA) (DG)(DA)(DT)(DG)(DA)(DC)(DG)(DA)(DG)(DG) (DC)(DA)(DT)(DT)(DT)(DG)(DG)(DC)(DT) (DA)(2DT)

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: THYMIDINE-5'-TRIPHOSPHATE

MacromoleculeName: THYMIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: TTP
Molecular weightTheoretical: 482.168 Da
Chemical component information

ChemComp-TTP:
THYMIDINE-5'-TRIPHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 441626
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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