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Open data
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Basic information
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Title | Structure of R2 with 5'ORF | |||||||||
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![]() | R2 complex / RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Reverse transcriptase (RNA-dependent DNA polymerase) / ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Deng P / Tan S / Wang J / Liu JJ | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural RNA components supervise the sequential DNA cleavage in R2 retrotransposon. Authors: Pujuan Deng / Shun-Qing Tan / Qi-Yu Yang / Liangzheng Fu / Yachao Wu / Han-Zhou Zhu / Lei Sun / Zhangbin Bao / Yi Lin / Qiangfeng Cliff Zhang / Haoyi Wang / Jia Wang / Jun-Jie Gogo Liu / ![]() Abstract: Retroelements are the widespread jumping elements considered as major drivers for genome evolution, which can also be repurposed as gene-editing tools. Here, we determine the cryo-EM structures of ...Retroelements are the widespread jumping elements considered as major drivers for genome evolution, which can also be repurposed as gene-editing tools. Here, we determine the cryo-EM structures of eukaryotic R2 retrotransposon with ribosomal DNA target and regulatory RNAs. Combined with biochemical and sequencing analysis, we reveal two essential DNA regions, Drr and Dcr, required for recognition and cleavage. The association of 3' regulatory RNA with R2 protein accelerates the first-strand cleavage, blocks the second-strand cleavage, and initiates the reverse transcription starting from the 3'-tail. Removing 3' regulatory RNA by reverse transcription allows the association of 5' regulatory RNA and initiates the second-strand cleavage. Taken together, our work explains the DNA recognition and RNA supervised sequential retrotransposition mechanisms by R2 machinery, providing insights into the retrotransposon and application reprogramming. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 14.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.6 KB 17.6 KB | Display Display | ![]() |
Images | ![]() | 94.7 KB | ||
Others | ![]() ![]() | 14.5 MB 14.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ibyMC ![]() 8ibwC ![]() 8ibxC ![]() 8ibzC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.0979 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_35349_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35349_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : R2 complex
Entire | Name: R2 complex |
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Components |
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-Supramolecule #1: R2 complex
Supramolecule | Name: R2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 177.28 KDa |
-Macromolecule #1: 5'ORF RNA
Macromolecule | Name: 5'ORF RNA / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 72.943172 KDa |
Sequence | String: UGUACACGUG GUAAACACGU GACAGCAGCC CCGAUGGACG GACCGCGAGG ACCGUCAAGC CUAGCAGGUA CCUUCGGGUG GGGCCUUGC GAUACCUGCG GGCGAACCCU GUGGUCGGGU UUGCAGCCCG GCCACAGUGG GUUUUUUUCC UGUUGCAAAA A AGUCAAAU ...String: UGUACACGUG GUAAACACGU GACAGCAGCC CCGAUGGACG GACCGCGAGG ACCGUCAAGC CUAGCAGGUA CCUUCGGGUG GGGCCUUGC GAUACCUGCG GGCGAACCCU GUGGUCGGGU UUGCAGCCCG GCCACAGUGG GUUUUUUUCC UGUUGCAAAA A AGUCAAAU AAAGAAAAUA GACCUACUGU GCGGGGUUCC GCCGGCGCUU GGACCUGCCA GUUCUGCG |
-Macromolecule #2: Reverse transcriptase-like protein
Macromolecule | Name: Reverse transcriptase-like protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 123.36243 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MMASTALSLM GRCNPDGCTR GKHVTAAPMD GPRGPSSLAG TFGWGLAIPA GEPCGRVCSP ATVGFFPVAK KSNKENRPEA SGLPLESER TGDNPTVRGS AGADPVGQDA PGWTCQFCER TFSTNRGLGV HKRRAHPVET NTDAAPMMVK RRWHGEEIDL L ARTEARLL ...String: MMASTALSLM GRCNPDGCTR GKHVTAAPMD GPRGPSSLAG TFGWGLAIPA GEPCGRVCSP ATVGFFPVAK KSNKENRPEA SGLPLESER TGDNPTVRGS AGADPVGQDA PGWTCQFCER TFSTNRGLGV HKRRAHPVET NTDAAPMMVK RRWHGEEIDL L ARTEARLL AERGQCSGGD LFGALPGFGR TLEAIKGQRR REPYRALVQA HLARFGSQPG PSSGGCSAEP DFRRASGAEE AG EERCAED AAAYDPSAVG QMSPDAARVL SELLEGAGRR RACRAMRPKT AGRRNDLHDD RTASAHKTSR QKRRAEYARV QEL YKKCRS RAAAEVIDGA CGGVGHSLEE METYWRPILE RVSDAPGPTP EALHALGRAE WHGGNRDYTQ LWKPISVEEI KASR FDWRT SPGPDGIRSG QWRAVPVHLK AEMFNAWMAR GEIPEILRQC RTVFVPKVER PGGPGEYRPI SIASIPLRHF HSILA RRLL ACCPPDARQR GFICADGTLE NSAVLDAVLG DSRKKLRECH VAVLDFAKAF DTVSHEALVE LLRLRGMPEQ FCGYIA HLY DTASTTLAVN NEMSSPVKVG RGVRQGDPLS PILFNVVMDL ILASLPERVG YRLEMELVSA LAYAYDLVLL AGSKVGM QE SISAVDCVGR QMGLRLNCRK SAVLSMIPDG HRKKHHYLTE RTFNIGGKPL RQVSCVERWR YLGVDFEASG CVTLEHSI S SALNNISRAP LKPQQRLEIL RAHLIPRFQH GFVLGNISDD RLRMLDVQIR KAVGQWLRLP ADVPKAYYHA AVQDGGLAI PSVRATIPDL IVRRFGGLDS SPWSVARAAA KSDKIRKKLR WAWKQLRRFS RVDSTTQRPS VRLFWREHLH ASVDGRELRE STRTPTSTK WIRERCAQIT GRDFVQFVHT HINALPSRIR GSRGRRGGGE SSLTCRAGCK VRETTAHILQ QCHRTHGGRI L RHNKIVSF VAKAMEENKW TVELEPRLRT SVGLRKPAII ASRDGVGVIV DVQVVSGQRS LDELHREKRN KYGNHGELVE LV AGRLGLP KAECVRATSC TISWRGVWSL TSYKELRSII GLREPTLQIV PILALRGSHM NWTRFNQMTS VMGGGVG UniProtKB: Reverse transcriptase-like protein |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE / Details: ab-initial in cryosparc |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |
Final 3D classification | Number classes: 3 / Software - Name: cryoSPARC (ver. 3.31) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.31) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 264298 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: BACKBONE TRACE |
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Output model | ![]() PDB-8iby: |