+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35595 | |||||||||
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Title | Cryo-EM structure of Cas12j-SF05-crRNA-dsDNA complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | CRISPR / RNA BINDING PROTEIN-RNA complex / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA-DNA complex | |||||||||
Biological species | Biggievirus Mos11 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Zhang X / Duan ZQ / Zhu JK | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Discov / Year: 2023 Title: Molecular basis for DNA cleavage by the hypercompact Cas12j-SF05. Authors: Zhiqiang Duan / Xi Zhang / Jun-Tao Zhang / Shanshan Li / Ruiheng Liu / Jie Sun / Qingzhi Zhao / Nannan Jia / Ning Jia / Jian-Kang Zhu / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35595.map.gz | 203.8 MB | EMDB map data format | |
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Header (meta data) | emd-35595-v30.xml emd-35595.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
Images | emd_35595.png | 51 KB | ||
Masks | emd_35595_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-35595.cif.gz | 6.1 KB | ||
Others | emd_35595_half_map_1.map.gz emd_35595_half_map_2.map.gz | 200.7 MB 200.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35595 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35595 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_35595.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.66 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_35595_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35595_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35595_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex of Cas12j-SF05 with crRNA and target dsDNA
Entire | Name: Ternary complex of Cas12j-SF05 with crRNA and target dsDNA |
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Components |
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-Supramolecule #1: Ternary complex of Cas12j-SF05 with crRNA and target dsDNA
Supramolecule | Name: Ternary complex of Cas12j-SF05 with crRNA and target dsDNA type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Biggievirus Mos11 |
-Macromolecule #1: Cas12j-SF05
Macromolecule | Name: Cas12j-SF05 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Biggievirus Mos11 |
Molecular weight | Theoretical: 83.449094 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MTPKTETPVG ALIKKFFPGK RFQKNYLKDA GKKLKREGEA AAVEYLSGKQ EDHPANFCPP AKVNILAQSR PLSEWPINLV SKGVQEYVY GLTAAEREAN GDFGTSRKSL DRWFARTGVP THGYTTVQGL NLILRHTFNR YDGVIKKVET RNEKRRSKAT R INVSREAD ...String: MTPKTETPVG ALIKKFFPGK RFQKNYLKDA GKKLKREGEA AAVEYLSGKQ EDHPANFCPP AKVNILAQSR PLSEWPINLV SKGVQEYVY GLTAAEREAN GDFGTSRKSL DRWFARTGVP THGYTTVQGL NLILRHTFNR YDGVIKKVET RNEKRRSKAT R INVSREAD GLPPIEAEPE ETAFGPDGKL KERPGINPSI YCYQQVSPVP YNPAKHPALP FSGVDPGAPL PLGTPNRLSI PK GQPGYVP EWQRPHLSTK NKRIRKWYAR ANWRRKPGRK SVLDEAKLKE AALKEAIPII VTIGKDWIVM DARGLLRAVY WRG IAKPGL SLKELLGFFS GDPVLDPKRG IATFTFKLGA VAVHSRKPTR GKKSKELLLS MTAEKPHVGL VAIDLGQTNP VAAE FSRVK REGETLQAEP LGQIVLPDDL VKDLTRYRRA WDATEEQIKA EAIVQLPEEC RAEVVKVNQM SAEETKHLIL DRGVS GDLP WEKMTSNTTF ISDHLLAKGV TDQVFFEKKS KGKKKGTETV KRKDYGWVKL LRPRLSQETR KAVNDKTWEL KRASTE YVR LSRRKTELAR RCVNYIVRET KRWTQCEDIA IVIEDLNVRF FHGSGERPDG WDNFFISKRE NRWFIQVLHK AFSDLAL HR GLPVIEANPA RTSITCIRCG HCDRNNRHGE MFLCLSCNDL RHADREIATR NLTRVAVTGE MIPRRIEPGE QSGDTKKA R SARKGKKAVI SKREAA |
-Macromolecule #2: crRNA
Macromolecule | Name: crRNA / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Biggievirus Mos11 |
Molecular weight | Theoretical: 18.179771 KDa |
Sequence | String: GCCGUCAACG UUCAACGCUU GCUCGGUUCG CCGAGACUCC CCUACGUGCU GCUGAAG |
-Macromolecule #3: TS-DNA
Macromolecule | Name: TS-DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Biggievirus Mos11 |
Molecular weight | Theoretical: 16.99491 KDa |
Sequence | String: (DG)(DA)(DA)(DT)(DT)(DG)(DA)(DA)(DG)(DC) (DT)(DG)(DC)(DC)(DC)(DT)(DT)(DG)(DC)(DA) (DA)(DC)(DT)(DT)(DC)(DA)(DG)(DC)(DA) (DG)(DC)(DA)(DC)(DG)(DT)(DA)(DG)(DG)(DG) (DG) (DA)(DG)(DA)(DA)(DT)(DT) ...String: (DG)(DA)(DA)(DT)(DT)(DG)(DA)(DA)(DG)(DC) (DT)(DG)(DC)(DC)(DC)(DT)(DT)(DG)(DC)(DA) (DA)(DC)(DT)(DT)(DC)(DA)(DG)(DC)(DA) (DG)(DC)(DA)(DC)(DG)(DT)(DA)(DG)(DG)(DG) (DG) (DA)(DG)(DA)(DA)(DT)(DT)(DG)(DG) (DC)(DC)(DA)(DC)(DA)(DC)(DA) |
-Macromolecule #4: NTS-DNA
Macromolecule | Name: NTS-DNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Biggievirus Mos11 |
Molecular weight | Theoretical: 16.900799 KDa |
Sequence | String: (DT)(DG)(DT)(DG)(DT)(DG)(DG)(DC)(DC)(DA) (DA)(DT)(DT)(DC)(DT)(DC)(DC)(DC)(DC)(DT) (DA)(DC)(DG)(DT)(DG)(DC)(DT)(DG)(DC) (DT)(DG)(DA)(DA)(DG)(DT)(DT)(DG)(DC)(DA) (DA) (DG)(DG)(DG)(DC)(DA)(DG) ...String: (DT)(DG)(DT)(DG)(DT)(DG)(DG)(DC)(DC)(DA) (DA)(DT)(DT)(DC)(DT)(DC)(DC)(DC)(DC)(DT) (DA)(DC)(DG)(DT)(DG)(DC)(DT)(DG)(DC) (DT)(DG)(DA)(DA)(DG)(DT)(DT)(DG)(DC)(DA) (DA) (DG)(DG)(DG)(DC)(DA)(DG)(DC)(DT) (DT)(DC)(DA)(DA)(DT)(DT)(DC) |
-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: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 59719 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |