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Yorodumi- EMDB-35912: Cryo-EM structure of the AsCas12f-sgRNA-target DNA ternary complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35912 | |||||||||
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Title | Cryo-EM structure of the AsCas12f-sgRNA-target DNA ternary complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | CRISPR-Cas / RNA BINDING PROTEIN-DNA COMPLEX / RNA BINDING PROTEIN / RNA BINDING PROTEIN-DNA-RNA complex | |||||||||
Function / homology | Transposase IS605, OrfB, C-terminal / Putative transposase DNA-binding domain / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding / CRISPR-associated endodeoxyribonuclease Cas12f1 Function and homology information | |||||||||
Biological species | Mycolicibacterium mucogenicum (bacteria) / Acidibacillus sulfuroxidans (bacteria) / Acidibacillus sulfooxidans (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.08 Å | |||||||||
Authors | Hino T / Omura NS / Nakagawa R / Togashi T / Takeda NS / Hiramoto T / Tasaka S / Hirano H / Tokuyama T / Uosaki H ...Hino T / Omura NS / Nakagawa R / Togashi T / Takeda NS / Hiramoto T / Tasaka S / Hirano H / Tokuyama T / Uosaki H / Ishiguro H / Yamano H / Ozaki Y / Motooka D / Mori H / Kirita Y / Kise Y / Itoh Y / Matoba S / Aburatani H / Yachie N / Siksnys V / Ohmori T / Hoshino A / Nureki O | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: To Be Published Title: Minimal and most efficient genome editing Cas enzyme Authors: Hino T / Omura NS / Nakagawa R / Togashi T / Takeda NS / Hiramoto T / Tasaka S / Hirano H / Tokuyama T / Uosaki H / Ishiguro H / Yamano H / Ozaki Y / Motooka D / Mori H / Kirita Y / Kise Y / ...Authors: Hino T / Omura NS / Nakagawa R / Togashi T / Takeda NS / Hiramoto T / Tasaka S / Hirano H / Tokuyama T / Uosaki H / Ishiguro H / Yamano H / Ozaki Y / Motooka D / Mori H / Kirita Y / Kise Y / Itoh Y / Matoba S / Aburatani H / Yachie N / Siksnys V / Ohmori T / Hoshino A / Nureki O | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35912.map.gz | 7.2 MB | EMDB map data format | |
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Header (meta data) | emd-35912-v30.xml emd-35912.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35912_fsc.xml | 6.6 KB | Display | FSC data file |
Images | emd_35912.png | 99.3 KB | ||
Others | emd_35912_half_map_1.map.gz emd_35912_half_map_2.map.gz | 7.1 MB 7.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35912 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35912 | HTTPS FTP |
-Related structure data
Related structure data | 8j12MC 8j1jC 8j3rC 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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-Map
File | Download / File: emd_35912.map.gz / Format: CCP4 / Size: 7.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.328 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_35912_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35912_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : AsCas12f-sgRNA-target DNA
Entire | Name: AsCas12f-sgRNA-target DNA |
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Components |
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-Supramolecule #1: AsCas12f-sgRNA-target DNA
Supramolecule | Name: AsCas12f-sgRNA-target DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Mycolicibacterium mucogenicum (bacteria) |
-Macromolecule #1: Transposase IS605 OrfB C-terminal domain-containing protein
Macromolecule | Name: Transposase IS605 OrfB C-terminal domain-containing protein type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Acidibacillus sulfuroxidans (bacteria) |
Molecular weight | Theoretical: 49.925008 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGHHHHHHGS MIKVYRYEIV KPLDLDWKEF GTILRQLQQE TRFALNKATQ LAWEWMGFSS DYKDNHGEYP KSKDILGYTN VHGYAYHTI KTKAYRLNSG NLSQTIKRAT DRFKAYQKEI LRGDMSIPSY KRDIPLDLIK ENISVNRMNH GDYIASLSLL S NPAKQEMN ...String: MGHHHHHHGS MIKVYRYEIV KPLDLDWKEF GTILRQLQQE TRFALNKATQ LAWEWMGFSS DYKDNHGEYP KSKDILGYTN VHGYAYHTI KTKAYRLNSG NLSQTIKRAT DRFKAYQKEI LRGDMSIPSY KRDIPLDLIK ENISVNRMNH GDYIASLSLL S NPAKQEMN VKRKISVIII VRGAGKTIMD RILSGEYQVS ASQIIHDDRK NKWYLNISYD FEPQTRVLDL NKIMGIDLGV AV AVYMAFQ HTPARYKLEG GEIENFRRQV ESRRISMLRQ GKYAGGARGG HGRDKRIKPI EQLRDKIANF RDTTNHRYSR YIV DMAIKE GCGTIQMEDL TNIRDIGSRF LQNWTYYDLQ QKIIYKAEEA GIKVIKIDPQ YTSQRCSECG NIDSGNRIGQ AIFK CRACG YEANADYNAA RNIAIPNIDK IIAESIK UniProtKB: CRISPR-associated endodeoxyribonuclease Cas12f1 |
-Macromolecule #2: DNA (38-MER)
Macromolecule | Name: DNA (38-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Acidibacillus sulfooxidans (bacteria) |
Molecular weight | Theoretical: 11.694576 KDa |
Sequence | String: (DG)(DA)(DA)(DT)(DG)(DG)(DT)(DT)(DC)(DA) (DA)(DG)(DC)(DG)(DC)(DA)(DC)(DC)(DT)(DA) (DA)(DT)(DT)(DT)(DC)(DC)(DT)(DA)(DA) (DA)(DT)(DT)(DA)(DG)(DA)(DA)(DA)(DA) |
-Macromolecule #3: DNA (38-MER)
Macromolecule | Name: DNA (38-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Acidibacillus sulfooxidans (bacteria) |
Molecular weight | Theoretical: 11.689535 KDa |
Sequence | String: (DT)(DT)(DT)(DT)(DC)(DT)(DA)(DA)(DT)(DT) (DT)(DA)(DG)(DG)(DA)(DA)(DA)(DT)(DT)(DA) (DG)(DG)(DT)(DG)(DC)(DG)(DC)(DT)(DT) (DG)(DA)(DA)(DC)(DC)(DA)(DT)(DT)(DC) |
-Macromolecule #4: RNA (247-MER)
Macromolecule | Name: RNA (247-MER) / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: Acidibacillus sulfooxidans (bacteria) |
Molecular weight | Theoretical: 72.329883 KDa |
Sequence | String: GGAUACUUCU AUUCGUCGGU UCAGCGACGA UAAGCCGAGA AGUGCCAAUA AAACUGUUAA GUGGUUUGGU AACGCUCGGU AAGGUAGCC AAAAGGCUGA AACUCCGUGC ACAAAGACCG CACGGACGCU UCACAUAUAG CUCAUAAACA AAUGUCGUCG A CCUCUAAU ...String: GGAUACUUCU AUUCGUCGGU UCAGCGACGA UAAGCCGAGA AGUGCCAAUA AAACUGUUAA GUGGUUUGGU AACGCUCGGU AAGGUAGCC AAAAGGCUGA AACUCCGUGC ACAAAGACCG CACGGACGCU UCACAUAUAG CUCAUAAACA AAUGUCGUCG A CCUCUAAU AGCGAAAGUU UGCGAGCUAG CUUGUGGAGU GUGAACGGAA AUUAGGUGCG CUUGGC |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 7 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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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: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |