+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24143 | |||||||||
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Title | Cryo-EM structure of the Cas12k-sgRNA-dsDNA complex | |||||||||
Map data | Cas12k-sgRNA-dsDNA complex | |||||||||
Sample |
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Biological species | Scytonema hofmannii (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.65 Å | |||||||||
Authors | Chang L / Li Z / Xiao R / Wang S / Han R | |||||||||
Citation | Journal: Mol Cell / Year: 2021 Title: Structural basis of target DNA recognition by CRISPR-Cas12k for RNA-guided DNA transposition. Authors: Renjian Xiao / Shukun Wang / Ruijie Han / Zhuang Li / Clinton Gabel / Indranil Arun Mukherjee / Leifu Chang / Abstract: The type V-K CRISPR-Cas system, featured by Cas12k effector with a naturally inactivated RuvC domain and associated with Tn7-like transposon for RNA-guided DNA transposition, is a promising tool for ...The type V-K CRISPR-Cas system, featured by Cas12k effector with a naturally inactivated RuvC domain and associated with Tn7-like transposon for RNA-guided DNA transposition, is a promising tool for precise DNA insertion. To reveal the mechanism underlying target DNA recognition, we determined a cryoelectron microscopy (cryo-EM) structure of Cas12k from cyanobacteria Scytonema hofmanni in complex with a single guide RNA (sgRNA) and a double-stranded target DNA. Coupled with mutagenesis and in vitro DNA transposition assay, our results revealed mechanisms for the recognition of the GGTT protospacer adjacent motif (PAM) sequence and the structural elements of Cas12k critical for RNA-guided DNA transposition. These structural and mechanistic insights should aid in the development of type V-K CRISPR-transposon systems as tools for genome editing. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24143.map.gz | 28.7 MB | EMDB map data format | |
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Header (meta data) | emd-24143-v30.xml emd-24143.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
Images | emd_24143.png | 107.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24143 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24143 | HTTPS FTP |
-Related structure data
Related structure data | 7n3pMC 7n3oC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_24143.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cas12k-sgRNA-dsDNA complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Cryo-EM structure of the Cas12k-sgRNA-dsDNA complex
Entire | Name: Cryo-EM structure of the Cas12k-sgRNA-dsDNA complex |
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Components |
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-Supramolecule #1: Cryo-EM structure of the Cas12k-sgRNA-dsDNA complex
Supramolecule | Name: Cryo-EM structure of the Cas12k-sgRNA-dsDNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Cas12k
Supramolecule | Name: Cas12k / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Scytonema hofmannii (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Supramolecule #3: single-guide RNA/Target DNA
Supramolecule | Name: single-guide RNA/Target DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#4 |
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Source (natural) | Organism: Scytonema hofmannii (bacteria) |
-Macromolecule #1: Cas12k
Macromolecule | Name: Cas12k / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Scytonema hofmannii (bacteria) |
Molecular weight | Theoretical: 73.280719 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSQITIQARL ISFESNRQQL WKLMADLNTP LINELLCQLG QHPDFEKWQQ KGKLPSTVVS QLCQPLKTDP RFAGQPSRLY MSAIHIVDY IYKSWLAIQK RLQQQLDGKT RWLEMLNSDA ELVELSGDTL EAIRVKAAEI LAIAMPASES DSASPKGKKG K KEKKPSSS ...String: MSQITIQARL ISFESNRQQL WKLMADLNTP LINELLCQLG QHPDFEKWQQ KGKLPSTVVS QLCQPLKTDP RFAGQPSRLY MSAIHIVDY IYKSWLAIQK RLQQQLDGKT RWLEMLNSDA ELVELSGDTL EAIRVKAAEI LAIAMPASES DSASPKGKKG K KEKKPSSS SPKRSLSKTL FDAYQETEDI KSRSAISYLL KNGCKLTDKE EDSEKFAKRR RQVEIQIQRL TEKLISRMPK GR DLTNAKW LETLLTATTT VAEDNAQAKR WQDILLTRSS SLPFPLVFET NEDMVWSKNQ KGRLCVHFNG LSDLIFEVYC GNR QLHWFQ RFLEDQQTKR KSKNQHSSGL FTLRNGHLVW LEGEGKGEPW NLHHLTLYCC VDNRLWTEEG TEIVRQEKAD EITK FITNM KKKSDLSDTQ QALIQRKQST LTRINNSFER PSQPLYQGQS HILVGVSLGL EKPATVAVVD AIANKVLAYR SIKQL LGDN YELLNRQRRQ QQYLSHERHK AQKNFSPNQF GASELGQHID RLLAKAIVAL ARTYKAGSIV LPKLGDMREV VQSEIQ AIA EQKFPGYIEG QQKYAKQYRV NVHRWSYGRL IQSIQSKAAQ TGIVIEEGKQ PIRGSPHDKA KELALSAYNL RLTRRS |
-Macromolecule #2: Single guide RNA
Macromolecule | Name: Single guide RNA / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Scytonema hofmannii (bacteria) |
Molecular weight | Theoretical: 85.26125 KDa |
Sequence | String: AUAUUAAUAG CGCCGCAAUU CAUGCUGCUU GCAGCCUCUG AAUUUUGUUA AAUGAGGGUU AGUUUGACUG UAUAAAUACA GUCUUGCUU UCUGACCCUG GUAGCUGCUC ACCCUGAUGC UGCUGUCAAU AGACAGGAUA GGUGCGCUCC CAGCAAUAAG G GCGCGGAU ...String: AUAUUAAUAG CGCCGCAAUU CAUGCUGCUU GCAGCCUCUG AAUUUUGUUA AAUGAGGGUU AGUUUGACUG UAUAAAUACA GUCUUGCUU UCUGACCCUG GUAGCUGCUC ACCCUGAUGC UGCUGUCAAU AGACAGGAUA GGUGCGCUCC CAGCAAUAAG G GCGCGGAU GUACUGCUGU AGUGGCUACU GAAUCACCCC CGAUCAAGGG GGAACCCUCC AAAAGGUGGG UUGAAAGGAG AA GUCAUUU AAUAAGGCCA CUGUUAAA |
-Macromolecule #3: DNA (5'-D(*CP*AP*TP*GP*AP*CP*TP*TP*CP*TP*CP*AP*AP*CP*CP*GP*AP*GP*...
Macromolecule | Name: DNA (5'-D(*CP*AP*TP*GP*AP*CP*TP*TP*CP*TP*CP*AP*AP*CP*CP*GP*AP*GP*TP*TP*T)-3') type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Scytonema hofmannii (bacteria) |
Molecular weight | Theoretical: 12.181854 KDa |
Sequence | String: (DT)(DT)(DA)(DA)(DC)(DA)(DG)(DT)(DG)(DG) (DC)(DC)(DT)(DT)(DA)(DT)(DT)(DA)(DA)(DA) (DT)(DG)(DA)(DC)(DT)(DT)(DC)(DT)(DC) (DA)(DA)(DC)(DC)(DT)(DC)(DC)(DT)(DA)(DC) (DG) |
-Macromolecule #4: DNA (5'-D(P*AP*AP*AP*CP*TP*CP*GP*GP*TP*T)-3')
Macromolecule | Name: DNA (5'-D(P*AP*AP*AP*CP*TP*CP*GP*GP*TP*T)-3') / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Scytonema hofmannii (bacteria) |
Molecular weight | Theoretical: 3.429245 KDa |
Sequence | String: (DC)(DG)(DT)(DA)(DG)(DG)(DA)(DG)(DG)(DT) (DT) |
-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: OTHER |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 3021295 |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114383 |