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- EMDB-47091: Taeniopygia guttata R2 retrotransposon (R2Tg) initiating target-p... -

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Basic information

Entry
Database: EMDB / ID: EMD-47091
TitleTaeniopygia guttata R2 retrotransposon (R2Tg) initiating target-primed reverse transcription
Map dataSharpened map of Taeniopygia guttata R2 retrotransposon initiating target-primed reverse transcription
Sample
  • Complex: Taeniopygia guttata R2 retrotransposon initiating target-primed reverse transcription
    • Protein or peptide: R2Tg retrotransposon ORF
    • DNA: 28S DNA bottom strand, 3' side
    • DNA: 28S DNA bottom strand, 5' side (priming strand)
    • RNA: R2Tg 3'UTR RNA
    • DNA: 28S DNA top strand
  • Ligand: MAGNESIUM ION
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
Keywordsretrotransposon / LINE / reverse transcriptase / endonuclease / RNA BINDING PROTEIN-RNA-DNA complex
Biological speciesTaeniopygia guttata (zebra finch)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWilkinson ME / Edmonds KHK / Zhang F
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Structure and biochemistry-guided engineering of an all-RNA system for DNA insertion with R2 retrotransposons
Authors: Edmonds KHK / Wilkinson ME / Strebinger D / Chen H / Lash B / Zhu S / Liu D / Zilberzwige-Tal S / Ladha A / Walsh ML / Frangieh CJ / Macrae R / Wang X / Zhang F
History
DepositionSep 19, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47091.png

Downloads & links

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Map

FileDownload / File: emd_47091.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of Taeniopygia guttata R2 retrotransposon initiating target-primed reverse transcription
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 288 pix.
= 265.19 Å		0.92 Å/pix.
x 288 pix.
= 265.19 Å		0.92 Å/pix.
x 288 pix.
= 265.19 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9208 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.049436692 - 0.09317815
Average (Standard dev.)-0.00010939993 (±0.003444031)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 265.1904 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47091_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 of Taeniopygia guttata R2 retrotransposon initiating...

Fileemd_47091_half_map_1.map
AnnotationHalf-map 2 of Taeniopygia guttata R2 retrotransposon initiating target-primed reverse transcription
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1 of Taeniopygia guttata R2 retrotransposon initiating...

Fileemd_47091_half_map_2.map
AnnotationHalf-map 1 of Taeniopygia guttata R2 retrotransposon initiating target-primed reverse transcription
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Taeniopygia guttata R2 retrotransposon initiating target-primed r...

EntireName: Taeniopygia guttata R2 retrotransposon initiating target-primed reverse transcription
Components
  • Complex: Taeniopygia guttata R2 retrotransposon initiating target-primed reverse transcription
    • Protein or peptide: R2Tg retrotransposon ORF
    • DNA: 28S DNA bottom strand, 3' side
    • DNA: 28S DNA bottom strand, 5' side (priming strand)
    • RNA: R2Tg 3'UTR RNA
    • DNA: 28S DNA top strand
  • Ligand: MAGNESIUM ION
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: Taeniopygia guttata R2 retrotransposon initiating target-primed r...

SupramoleculeName: Taeniopygia guttata R2 retrotransposon initiating target-primed reverse transcription
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Taeniopygia guttata (zebra finch)
Molecular weightTheoretical: 380 KDa

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Macromolecule #1: R2Tg retrotransposon ORF

MacromoleculeName: R2Tg retrotransposon ORF / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Taeniopygia guttata (zebra finch)
Molecular weightTheoretical: 157.228484 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MASCPKPGPP VSAGAMSLES GLTTHSVLAI ERGPNSLANS GSDFGGGGLG LPLRLLRVSV GTQTSRSDWV DLVSWSHPGP TSKSQQVDL VSLFPKHRVD LLSKNDQVDL VAQFLPSKFP PNLAENDLAL LVNLEFYRSD LHVYECVHFA AHWEGLSGLP E VYEQLAPQ ...String:
MASCPKPGPP VSAGAMSLES GLTTHSVLAI ERGPNSLANS GSDFGGGGLG LPLRLLRVSV GTQTSRSDWV DLVSWSHPGP TSKSQQVDL VSLFPKHRVD LLSKNDQVDL VAQFLPSKFP PNLAENDLAL LVNLEFYRSD LHVYECVHFA AHWEGLSGLP E VYEQLAPQ PCVGETLHSS LPRDSELFVP EEGSSEKESE DAPKTSPPTP GKHGLEQTGE EKVMVTVPDK NPPCPCCGTR VN SVLNLIE HLKVSHGKRG VCFRCAKCGK ENSNYHSVVC HFPKCRGPET EKAPAGEWIC EVCNRDFTTK IGLGQHKRLA HPA VRNQER IVASQPKETS NRGAHKRCWT KEEEELLIRL EAQFEGNKNI NKLIAEHITT KTAKQISDKR RLLSRKPAEE PREE PGTCH HTRRAAASLR TEPEMSHHAQ AEDRDNGPGR RPLPGRAAAG GRTMDEIRRH PDKGNGQQRP TKQKSEEQLQ AYYKK TLEE RLSAGALNTF PRAFKQVMEG RDIKLVINQT AQDCFGCLES ISQIRTATRD KKDTVTREKH PKKPFQKWMK DRAIKK GNY LRFQRLFYLD RGKLAKIILD DIECLSCDIP LSEIYSVFKT RWETTGSFKS LGDFKTYGKA DNTAFRELIT AKEIEKN VQ EMSKGSAPGP DGITLGDVVK MDPEFSRTME IFNLWLTTGK IPDMVRGCRT VLIPKSSKPD RLKDINNWRP ITIGSILL R LFSRIVTARL SKACPLNPRQ RGFIRAAGCS ENLKLLQTII WSAKREHRPL GVVFVDIAKA FDTVSHQHII HALQQREVD PHIVGLVSNM YENISTYITT KRNTHTDKIQ IRVGVKQGDP MSPLLFNLAM DPLLCKLEES GKGYHRGQSS ITAMAFADDL VLLSDSWEN MNTNISILET FCNLTGLKTQ GQKCHGFYIK PTKDSYTIND CAAWTINGTP LNMIDPGESE KYLGLQFDPW I GIARSGLS TKLDFWLQRI DQAPLKPLQK TDILKTYTIP RLIYIADHSE VKTALLETLD QKIRTAVKEW LHLPPCTCDA IL YSSTRDG GLGITKLAGL IPSVQARRLH RIAQSSDDTM KCFMEKEKME QLHKKLWIQA GGDRENIPSI WEAPPSSEPP NNV STNSEW EAPTQKDKFP KPCNWRKNEF KKWTKLASQG RGIVNFERDK ISNHWIQYYR RIPHRKLLTA LQLRANVYPT REFL ARGRQ DQYIKACRHC DADIESCAHI IGNCPVTQDA RIKRHNYICE LLLEEAKKKD WVVFKEPHIR DSNKELYKPD LIFVK DARA LVVDVTVRYE AAKSSLEEAA AEKVRKYKHL ETEVRHLTNA KDVTFVGFPL GARGKWHQDN FKLLTELGLS KSRQVK MAE TFSTVALFSS VDIVHMFASR ARKSMVM

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Macromolecule #2: 28S DNA bottom strand, 3' side

MacromoleculeName: 28S DNA bottom strand, 3' side / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Taeniopygia guttata (zebra finch)
Molecular weightTheoretical: 65.051477 KDa
SequenceString: (DT)(DT)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC) (DT)(DG)(DT)(DG)(DG)(DT)(DT)(DT)(DC)(DG) (DC)(DT)(DA)(DG)(DA)(DT)(DA)(DG)(DT) (DA)(DG)(DA)(DT)(DA)(DG)(DG)(DG)(DA)(DC) (DA) (DG)(DT)(DG)(DG)(DG)(DA) ...String:
(DT)(DT)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC) (DT)(DG)(DT)(DG)(DG)(DT)(DT)(DT)(DC)(DG) (DC)(DT)(DA)(DG)(DA)(DT)(DA)(DG)(DT) (DA)(DG)(DA)(DT)(DA)(DG)(DG)(DG)(DA)(DC) (DA) (DG)(DT)(DG)(DG)(DG)(DA)(DA)(DT) (DC)(DT)(DC)(DG)(DT)(DT)(DA)(DA)(DT)(DC) (DC)(DA) (DT)(DT)(DC)(DA)(DT)(DG)(DC) (DG)(DC)(DG)(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) (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)(DT)(DT)(DC) (DT)(DT)(DC)(DA)(DC)(DT)(DT) (DT)(DG) (DA)(DC)(DA)(DT)(DT)(DC)(DA)(DG)(DA)(DG) (DC)(DA)(DC)(DT)(DG)(DG)(DG)(DC) (DA) (DG)(DA)(DA)(DA)(DT)(DC)(DA)(DC)(DA)(DT) (DC)(DG)(DC)(DG)(DT)(DC)(DA)(DA)(DC) (DC)(DA)(DG)(DC)(DT)(DG)(DA)(DA)(DA)(DA) (DA)

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Macromolecule #3: 28S DNA bottom strand, 5' side (priming strand)

MacromoleculeName: 28S DNA bottom strand, 5' side (priming strand) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Taeniopygia guttata (zebra finch)
Molecular weightTheoretical: 3.997607 KDa
SequenceString:
(DG)(DG)(DC)(DA)(DT)(DT)(DT)(DG)(DG)(DC) (DT)(DA)(DT)

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Macromolecule #5: 28S DNA top strand

MacromoleculeName: 28S DNA top strand / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Taeniopygia guttata (zebra finch)
Molecular weightTheoretical: 65.225641 KDa
SequenceString: (DT)(DT)(DT)(DT)(DT)(DC)(DA)(DG)(DC)(DT) (DG)(DG)(DT)(DT)(DG)(DA)(DC)(DG)(DC)(DG) (DA)(DT)(DG)(DT)(DG)(DA)(DT)(DT)(DT) (DC)(DT)(DG)(DC)(DC)(DC)(DA)(DG)(DT)(DG) (DC) (DT)(DC)(DT)(DG)(DA)(DA) ...String:
(DT)(DT)(DT)(DT)(DT)(DC)(DA)(DG)(DC)(DT) (DG)(DG)(DT)(DT)(DG)(DA)(DC)(DG)(DC)(DG) (DA)(DT)(DG)(DT)(DG)(DA)(DT)(DT)(DT) (DC)(DT)(DG)(DC)(DC)(DC)(DA)(DG)(DT)(DG) (DC) (DT)(DC)(DT)(DG)(DA)(DA)(DT)(DG) (DT)(DC)(DA)(DA)(DA)(DG)(DT)(DG)(DA)(DA) (DG)(DA) (DA)(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)(DC)(DG) (DC)(DG)(DC)(DA)(DT)(DG)(DA)(DA)(DT)(DG) (DG)(DA)(DT)(DT)(DA)(DA)(DC) (DG)(DA) (DG)(DA)(DT)(DT)(DC)(DC)(DC)(DA)(DC)(DT) (DG)(DT)(DC)(DC)(DC)(DT)(DA)(DT) (DC) (DT)(DA)(DC)(DT)(DA)(DT)(DC)(DT)(DA)(DG) (DC)(DG)(DA)(DA)(DA)(DC)(DC)(DA)(DC) (DA)(DG)(DC)(DC)(DA)(DA)(DG)(DG)(DG)(DA) (DA)

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Macromolecule #4: R2Tg 3'UTR RNA

MacromoleculeName: R2Tg 3'UTR RNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Taeniopygia guttata (zebra finch)
Molecular weightTheoretical: 106.656273 KDa
SequenceString: UUCAGGUUAU UUAGAUGCUU AGUUUUUGUA CCUUUCUUGU UUUGUUUAGG AUUUUGAUAG UGUUAGUAUU UUUAUAUUUU UGUACGAUU GCAUAAUGUU CUUUUUUAUA CAGUUCUGUU UUAAUAAAAU AGACGAUAGC UAGAGACGUU AGGGCAGCCA C AAGCCAGU ...String:
UUCAGGUUAU UUAGAUGCUU AGUUUUUGUA CCUUUCUUGU UUUGUUUAGG AUUUUGAUAG UGUUAGUAUU UUUAUAUUUU UGUACGAUU GCAUAAUGUU CUUUUUUAUA CAGUUCUGUU UUAAUAAAAU AGACGAUAGC UAGAGACGUU AGGGCAGCCA C AAGCCAGU UAGGUAGCGG AUAGUAGGUA GGAACAGACU UUUACUAUUU CAUAACGCGU CAAUUACCAC CUGAUUUGGA CC AAUUCAC GGGAUUUGUC CAAGGUGGAC GGGCCACCUU UACUUAACCC GGAAAAGGAA CAUAUAUAAU UUAUGUGUGU UCG AUAAAU AGCCAAA

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: THYMIDINE-5'-TRIPHOSPHATE

MacromoleculeName: THYMIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: TTP
Molecular weightTheoretical: 482.168 Da
Chemical component information

ChemComp-TTP:
THYMIDINE-5'-TRIPHOSPHATE

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.9
Details: 20 mM HEPES-KOH pH 7.9, 400 mM potassium acetate, 5 mM magnesium acetate, 0.1 mM dTTP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV
DetailsA260 = 17

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 10627 / Average exposure time: 1.02 sec. / Average electron dose: 59.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 323700
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 30612
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9dou:
Taeniopygia guttata R2 retrotransposon (R2Tg) initiating target-primed reverse transcription

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