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Yorodumi- EMDB-27533: Structure of Desulfovirgula thermocuniculi IsrB (DtIsrB) in compl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27533 | |||||||||
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Title | Structure of Desulfovirgula thermocuniculi IsrB (DtIsrB) in complex with omega RNA and target DNA | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / condensed nuclear chromosome / protein tag activity / identical protein binding / nucleus Similarity search - Function | |||||||||
Biological species | synthetic construct (others) / Desulfovirgula thermocuniculi (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Seiichi H / Kappel K / Zhang F | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2022 Title: Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA. Authors: Seiichi Hirano / Kalli Kappel / Han Altae-Tran / Guilhem Faure / Max E Wilkinson / Soumya Kannan / F Esra Demircioglu / Rui Yan / Momoko Shiozaki / Zhiheng Yu / Kira S Makarova / Eugene V ...Authors: Seiichi Hirano / Kalli Kappel / Han Altae-Tran / Guilhem Faure / Max E Wilkinson / Soumya Kannan / F Esra Demircioglu / Rui Yan / Momoko Shiozaki / Zhiheng Yu / Kira S Makarova / Eugene V Koonin / Rhiannon K Macrae / Feng Zhang / Abstract: RNA-guided systems, such as CRISPR-Cas, combine programmable substrate recognition with enzymatic function, a combination that has been used advantageously to develop powerful molecular technologies. ...RNA-guided systems, such as CRISPR-Cas, combine programmable substrate recognition with enzymatic function, a combination that has been used advantageously to develop powerful molecular technologies. Structural studies of these systems have illuminated how the RNA and protein jointly recognize and cleave their substrates, guiding rational engineering for further technology development. Recent work identified a new class of RNA-guided systems, termed OMEGA, which include IscB, the likely ancestor of Cas9, and the nickase IsrB, a homologue of IscB lacking the HNH nuclease domain. IsrB consists of only around 350 amino acids, but its small size is counterbalanced by a relatively large RNA guide (roughly 300-nt ωRNA). Here, we report the cryogenic-electron microscopy structure of Desulfovirgula thermocuniculi IsrB (DtIsrB) in complex with its cognate ωRNA and a target DNA. We find the overall structure of the IsrB protein shares a common scaffold with Cas9. In contrast to Cas9, however, which uses a recognition (REC) lobe to facilitate target selection, IsrB relies on its ωRNA, part of which forms an intricate ternary structure positioned analogously to REC. Structural analyses of IsrB and its ωRNA as well as comparisons to other RNA-guided systems highlight the functional interplay between protein and RNA, advancing our understanding of the biology and evolution of these diverse systems. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27533.map.gz | 19.5 MB | EMDB map data format | |
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Header (meta data) | emd-27533-v30.xml emd-27533.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27533_fsc.xml | 6.3 KB | Display | FSC data file |
Images | emd_27533.png | 65.5 KB | ||
Others | emd_27533_half_map_1.map.gz emd_27533_half_map_2.map.gz | 15.9 MB 15.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27533 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27533 | HTTPS FTP |
-Related structure data
Related structure data | 8dmbMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27533.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.144 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_27533_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27533_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : DtIsrB-wRNA-tgDNA complex
Entire | Name: DtIsrB-wRNA-tgDNA complex |
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Components |
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-Supramolecule #1: DtIsrB-wRNA-tgDNA complex
Supramolecule | Name: DtIsrB-wRNA-tgDNA complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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-Macromolecule #1: Ubiquitin-like protein SMT3,IsrB protein,monomeric superfolder Gr...
Macromolecule | Name: Ubiquitin-like protein SMT3,IsrB protein,monomeric superfolder Green Fluorescent Protein type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 84.080859 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MASWSHPQFE KGGGSGGGSG GSAWSHPQFE KMSDSEVNQE AKPEVKPEVK PETHINLKVS DGSSEIFFK IKKTTPLRRL MEAFAKRQGK EMDSLRFLYD GIRIQADQTP EDLDMEDNDI IEAHREQIGG SMSTSITRVP V VGVDGRPL ...String: MGSSHHHHHH SSGLVPRGSH MASWSHPQFE KGGGSGGGSG GSAWSHPQFE KMSDSEVNQE AKPEVKPEVK PETHINLKVS DGSSEIFFK IKKTTPLRRL MEAFAKRQGK EMDSLRFLYD GIRIQADQTP EDLDMEDNDI IEAHREQIGG SMSTSITRVP V VGVDGRPL MPTTPRKARL LIRDGLAVPR RNKLGLFYIQ MLRPVGTRTQ PVALAVDPGA KYDGVAVASH RRVELRAMVF LP DDVPRKM ETRRNLRRAR RYRKTPRRPA RFDNRRRKGY WLAPTQRFKV EARLKVVREL CRIYPVQLIV TEDVRFNHAR DRN GKYFST VEIGKTLTYR EYRKLAELRL VEVSETDAWR ERFGLEKRTE RKCEQVPETH ANDAAAMLMG VTGCAHNPAA PFFV WRRLR YARRSLFRQN PQKDGVRPRF GGTANGGFFR KGDWVEAEKA GKVYRGWVCG LPTETTKLVG VADADGKRIG QFSPK KVRL LARSTGFSWK EVAAHSSPEV SKGEELFTGV VPILVELDGD VNGHKFSVRG EGEGDATNGK LTLKFICTTG KLPVPW PTL VTTLTYGVQC FSRYPDHMKQ HDFFKSAMPE GYVQERTISF KDDGTYKTRA EVKFEGDTLV NRIELKGIDF KEDGNIL GH KLEYNFNSHN VYITADKQKN GIKANFKIRH NVEDGSVQLA DHYQQNTPIG DGPVLLPDNH YLSTQSKLSK DPNEKRDH M VLLEFVTAAG ITLGMDELYK |
-Macromolecule #2: omega RNA
Macromolecule | Name: omega RNA / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Desulfovirgula thermocuniculi (bacteria) |
Molecular weight | Theoretical: 91.748258 KDa |
Sequence | String: GGGCCUUAUU AAAUGACUUC UCGUCAACCA CCCCUGACUG AAGUCAGAGG CUUGCUUCUG GCCUGAGUUG GGGGCCCGGU UUGGCGGGG CCGGGGGCAA CUGGCUGACC AGGCGGCCCG GUUCGCCGGG CAGGGGUCCG CGGGGCUACC AAGGACUUCC G GGUGUUUC ...String: GGGCCUUAUU AAAUGACUUC UCGUCAACCA CCCCUGACUG AAGUCAGAGG CUUGCUUCUG GCCUGAGUUG GGGGCCCGGU UUGGCGGGG CCGGGGGCAA CUGGCUGACC AGGCGGCCCG GUUCGCCGGG CAGGGGUCCG CGGGGCUACC AAGGACUUCC G GGUGUUUC GCCAGCCCGG ACUAUCUCCG GCAGAACCGC UCAAUGCCGC GGCCGGCCAA GACCGGCCUA AGCCCUGCGG AC AGCGCCG AGGCGACAAU CACUCCGAAA GGAGGCCGUG UAUCGGC |
-Macromolecule #3: target DNA
Macromolecule | Name: target DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 9.593223 KDa |
Sequence | String: (DG)(DA)(DT)(DC)(DA)(DG)(DC)(DT)(DC)(DA) (DA)(DG)(DA)(DG)(DA)(DA)(DG)(DT)(DC)(DA) (DT)(DT)(DT)(DA)(DA)(DT)(DA)(DA)(DG) (DG)(DC) |
-Macromolecule #4: non-target DNA
Macromolecule | Name: non-target DNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 3.075026 KDa |
Sequence | String: (DT)(DT)(DG)(DA)(DG)(DC)(DT)(DG)(DA)(DT) |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / 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 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.2 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |