[English] 日本語
Yorodumi
- EMDB-64055: Cryo-EM structure of R2Tg bound to template RNA and target DNA in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64055
TitleCryo-EM structure of R2Tg bound to template RNA and target DNA in the target-primed reverse transcription initiation state (state 2)
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
  • Ligand: water
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: 2.54 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: Nat Struct Mol Biol / Year: 2026
Title: Structural mechanism of programmable gene integration by the R2 retrotransposon coupled with CRISPR-Cas9.
Authors: Daisuke Komatsu / Masahiro Hiraizumi / Christopher W Fell / Kenta Fujimatsu / Naoto Nagahata / Sota Yamada / Sworaj Sapkota / Harsh Ramani / Benjamin Arya / Mikihiro Shibata / Keitaro ...Authors: Daisuke Komatsu / Masahiro Hiraizumi / Christopher W Fell / Kenta Fujimatsu / Naoto Nagahata / Sota Yamada / Sworaj Sapkota / Harsh Ramani / Benjamin Arya / Mikihiro Shibata / Keitaro Yamashita / Jonathan S Gootenberg / Omar O Abudayyeh / Hiroshi Nishimasu /
Abstract: R2 retroelements are non-long-terminal-repeat retrotransposons that primarily insert into 28S ribosomal DNA loci across diverse eukaryotes. R2 elements home to their target sites through target- ...R2 retroelements are non-long-terminal-repeat retrotransposons that primarily insert into 28S ribosomal DNA loci across diverse eukaryotes. R2 elements home to their target sites through target-primed reverse transcription (TPRT), in which the R2 protein recognizes and nicks the target DNA to prime reverse transcription using an R2-encoding RNA as the template. The avian R2 system from Taeniopygia guttata (R2Tg) can insert a payload sequence within an RNA template into 28S ribosomal DNA loci in human cells. Here, we present cryo-electron microscopy structures of the R2Tg-template RNA-target DNA complex in the TPRT initiation state, both alone and bound to a Cas9-guide RNA complex. These structures provide mechanistic insights into R2Tg-mediated TPRT in its natural context and in the programmable gene integration system STITCHR (site-specific target-primed insertion through targeted CRISPR homing of retroelements). Furthermore, we combine these structural insights with computational protein design methods to engineer an enhanced STITCHR system.
History
DepositionApr 6, 2025-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateNov 11, 2026-
Current statusNov 11, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_64055.png

Downloads & links

-
Map

FileDownload / File: emd_64055.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)

Slices (1/2)

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-0.1353717 - 0.33309034
Average (Standard dev.)-0.0002957157 (±0.0063809785)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_64055_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_64055_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_64055_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
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
  • Ligand: water

+
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)

+
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

+
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

+
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

+
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)

+
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)

+
Macromolecule #6: ZINC ION

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

+
Macromolecule #7: MAGNESIUM ION

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

+
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

+
Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 156 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 472858
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more