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- EMDB-36777: The Anoxybacillus pushchinoensis ORF-less Group IIC Intron DR1 at... -
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Open data
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Basic information
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Title | The Anoxybacillus pushchinoensis ORF-less Group IIC Intron DR1 at symmetric pre-cleavage state | |||||||||
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![]() | ORF-less Group IIC intron / ribozymes / ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Zhu HZ / Liu JJG | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 450.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.9 KB 15.9 KB | Display Display | ![]() |
Images | ![]() | 59.3 KB | ||
Filedesc metadata | ![]() | 5.2 KB | ||
Others | ![]() ![]() | 442.8 MB 442.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8k0qMC ![]() 8k0pC ![]() 8k0rC ![]() 8k0sC ![]() 8k15C M: atomic model generated by this map C: citing same article ( |
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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: 1.0825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36777_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36777_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : The Anoxybacillus pushchinoensis ORF-less Group IIC Intron HYER1 ...
Entire | Name: The Anoxybacillus pushchinoensis ORF-less Group IIC Intron HYER1 at symmetric pre-cleavage state |
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Components |
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-Supramolecule #1: The Anoxybacillus pushchinoensis ORF-less Group IIC Intron HYER1 ...
Supramolecule | Name: The Anoxybacillus pushchinoensis ORF-less Group IIC Intron HYER1 at symmetric pre-cleavage state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
-Supramolecule #2: RNA
Supramolecule | Name: RNA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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-Supramolecule #3: DNA
Supramolecule | Name: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Macromolecule #1: RNA (542-MER)
Macromolecule | Name: RNA (542-MER) / type: rna / ID: 1 / Number of copies: 2 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 205.134922 KDa |
Sequence | String: GUGCGCUCGG CAUGGGUGCA AUCUCUAGGG UGAAAGUCCC GAACUGCGAA GGCAGAAGUA GCAGUUAGCU UAACGCAAGG GUGUCCGUG GUGACGCGGA AUCUGAAGGA AGCGGGCGGC AAACUUCCGG UCUGAGGAAC ACGAACUUCA UAUAAGGCUA G GUAUCAUU ...String: GUGCGCUCGG CAUGGGUGCA AUCUCUAGGG UGAAAGUCCC GAACUGCGAA GGCAGAAGUA GCAGUUAGCU UAACGCAAGG GUGUCCGUG GUGACGCGGA AUCUGAAGGA AGCGGGCGGC AAACUUCCGG UCUGAGGAAC ACGAACUUCA UAUAAGGCUA G GUAUCAUU GGAUGAGUUU GCAAGACAAA ACAAAGUCCU UUCUGCCGAA GGUGAUACAG AGUAAAUGAA GCAGAUAGAU GG AAGGAAA GAUUGUACUC UUACCCGAGG AGGUCUGAUG GAUACGUGAA GUGCGCUUCA UAACCUACUU AGUGAUAAGU AAC UGAACC AUCAGAAGUC AGCAGAGGUC AUAGUACGAA UCGGUCUAGA ACGAUUCGGA AGGACUGAAC AAUCAAGAGA AAAU AGCCC UUGGCAUUCA GUACGUCAUG AUGAACACAG AAAACAUGGU ACCUCCCAAG AGAAAGGAAA CGGUGAAUCC CGUGG GAAU CUUUUGGAGG GUGGAGUGAC GACUGGCAUA AGAAGAUCAG CUAUUUACGG AAGGAAGCUU GCGUCAUUAU CUUGAU UGA ACCGCCGUAU ACGGAACCGU ACGUACGGUG GUGUGAGAGG ACGGAGGUUA AUCACCUCCU CCUACUCGAU |
-Macromolecule #2: DNA
Macromolecule | Name: DNA / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 2.672758 KDa |
Sequence | String: (DT)(DG)(DT)(DC)(DT)(DT)(DT)(DC)(DC) |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
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: OTHER |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 153769 |