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Yorodumi- EMDB-36786: The Streptococcus azizii ORF-less Group IIC intron HYER2 at apo state -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36786 | |||||||||
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Title | The Streptococcus azizii ORF-less Group IIC intron HYER2 at apo state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ORF-less Group IIC intron / ribozymes / RNA | |||||||||
Biological species | Streptococcus azizii (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.58 Å | |||||||||
Authors | Zhu HZ / Liu JJG | |||||||||
Funding support | China, 1 items
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Citation | Journal: Science / Year: 2024 Title: Hydrolytic endonucleolytic ribozyme (HYER) is programmable for sequence-specific DNA cleavage. Authors: Zi-Xian Liu / Shouyue Zhang / Han-Zhou Zhu / Zhi-Hang Chen / Yun Yang / Long-Qi Li / Yuan Lei / Yun Liu / Dan-Yuan Li / Ao Sun / Cheng-Ping Li / Shun-Qing Tan / Gao-Li Wang / Jie-Yi Shen / ...Authors: Zi-Xian Liu / Shouyue Zhang / Han-Zhou Zhu / Zhi-Hang Chen / Yun Yang / Long-Qi Li / Yuan Lei / Yun Liu / Dan-Yuan Li / Ao Sun / Cheng-Ping Li / Shun-Qing Tan / Gao-Li Wang / Jie-Yi Shen / Shuai Jin / Caixia Gao / Jun-Jie Gogo Liu / Abstract: Ribozymes are catalytic RNAs with diverse functions including self-splicing and polymerization. This work aims to discover natural ribozymes that behave as hydrolytic and sequence-specific DNA ...Ribozymes are catalytic RNAs with diverse functions including self-splicing and polymerization. This work aims to discover natural ribozymes that behave as hydrolytic and sequence-specific DNA endonucleases, which could be repurposed as DNA manipulation tools. Focused on bacterial group II-C introns, we found that many systems without intron-encoded protein propagate multiple copies in their resident genomes. These introns, named HYdrolytic Endonucleolytic Ribozymes (HYERs), cleaved RNA, single-stranded DNA, bubbled double-stranded DNA (dsDNA), and plasmids in vitro. HYER1 generated dsDNA breaks in the mammalian genome. Cryo-electron microscopy analysis revealed a homodimer structure for HYER1, where each monomer contains a Mg-dependent hydrolysis pocket and captures DNA complementary to the target recognition site (TRS). Rational designs including TRS extension, recruiting sequence insertion, and heterodimerization yielded engineered HYERs showing improved specificity and flexibility for DNA manipulation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36786.map.gz | 97.3 MB | EMDB map data format | |
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Header (meta data) | emd-36786-v30.xml emd-36786.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_36786.png | 38 KB | ||
Filedesc metadata | emd-36786.cif.gz | 5.1 KB | ||
Others | emd_36786_half_map_1.map.gz emd_36786_half_map_2.map.gz | 95.6 MB 95.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36786 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36786 | HTTPS FTP |
-Validation report
Summary document | emd_36786_validation.pdf.gz | 746.2 KB | Display | EMDB validaton report |
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Full document | emd_36786_full_validation.pdf.gz | 745.8 KB | Display | |
Data in XML | emd_36786_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | emd_36786_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36786 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36786 | HTTPS FTP |
-Related structure data
Related structure data | 8k15MC 8k0pC 8k0qC 8k0rC 8k0sC M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_36786.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0825 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36786_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36786_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The Streptococcus azizii ORF-less Group IIC intron HYER2 at apo state
Entire | Name: The Streptococcus azizii ORF-less Group IIC intron HYER2 at apo state |
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Components |
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-Supramolecule #1: The Streptococcus azizii ORF-less Group IIC intron HYER2 at apo state
Supramolecule | Name: The Streptococcus azizii ORF-less Group IIC intron HYER2 at apo state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Streptococcus azizii (bacteria) |
-Macromolecule #1: RNA (470-MER)
Macromolecule | Name: RNA (470-MER) / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: Streptococcus azizii (bacteria) |
Molecular weight | Theoretical: 201.116625 KDa |
Sequence | String: GUACGACGGG CAUGUCGUAC AUCUGAGGUG CAAGUCCUCU GUGGACACCU GCUACCGGUG AACCCAAUAG CGACUCCCAA GCCUGACUA UCGCGAGGUA ACGGGGAGAG GAAGGGAUAG CGAAAUCGUG GCUCUACGAA CAGAAACGUG AUAUUAAGGC G UAUAUAGU ...String: GUACGACGGG CAUGUCGUAC AUCUGAGGUG CAAGUCCUCU GUGGACACCU GCUACCGGUG AACCCAAUAG CGACUCCCAA GCCUGACUA UCGCGAGGUA ACGGGGAGAG GAAGGGAUAG CGAAAUCGUG GCUCUACGAA CAGAAACGUG AUAUUAAGGC G UAUAUAGU GGAUGAGGGG GCUAGGCACU CUAAAGUCCA AAAAGGUAGU CGUAAUCUAU GUGCGUAAAU CACGAGAGUA AA CGAGGAA AGAUGUACGA CUUAUCCCGU GAGGUCUCAU GAGCGUCAAG UAGACGUAGU AAUAACGAAU CAUGAGAAGU CAG CCGAGG UCAUAGUAGU GAUGAAGUUU CUGUAAUGGA AACGGAGCGA AGGACCGAAC GAUUAAAUGA UACCCUAUCU AACU GAUUU UGUCUGCCCU AACACCUGGU CUGAAAUGAC GGUACUCGCA GAACGUAUGC UGAAAGAGGC UGCUCACAAA UAUAG GACG GCACAAGCGG AACGAAAUCA UAUAUAGGUA GGUGUGGGAA CAAAAAAAGU GUUCUCGCCA AAGUUUAGUU GAACCG CCG UGUGCCGAAC GGCACGCACG GUGGUGUGAG AGGGACUAUC AAUUAGUCCC UACUCGAU |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 335884 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |