+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27320 | |||||||||
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Title | Cryo-EM structure of CasLambda (Cas12l) bound to crRNA and DNA | |||||||||
Map data | LocSpiral map from cryoSPARC half maps | |||||||||
Sample |
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Keywords | CRISPR / RNA Binding Protein / DNA binding protein / phage / viral protein / enzyme / ribonucleoprotein / RNA BINDING PROTEIN-RNA-DNA complex | |||||||||
Biological species | uncultured virus (environmental samples) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.99 Å | |||||||||
Authors | Al-Shayeb B / Skopintsev P / Soczek K / Doudna J | |||||||||
Funding support | United States, Switzerland, 2 items
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Citation | Journal: Cell / Year: 2022 Title: Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors. Authors: Basem Al-Shayeb / Petr Skopintsev / Katarzyna M Soczek / Elizabeth C Stahl / Zheng Li / Evan Groover / Dylan Smock / Amy R Eggers / Patrick Pausch / Brady F Cress / Carolyn J Huang / Brian ...Authors: Basem Al-Shayeb / Petr Skopintsev / Katarzyna M Soczek / Elizabeth C Stahl / Zheng Li / Evan Groover / Dylan Smock / Amy R Eggers / Patrick Pausch / Brady F Cress / Carolyn J Huang / Brian Staskawicz / David F Savage / Steven E Jacobsen / Jillian F Banfield / Jennifer A Doudna / Abstract: CRISPR-Cas systems are host-encoded pathways that protect microbes from viral infection using an adaptive RNA-guided mechanism. Using genome-resolved metagenomics, we find that CRISPR systems are ...CRISPR-Cas systems are host-encoded pathways that protect microbes from viral infection using an adaptive RNA-guided mechanism. Using genome-resolved metagenomics, we find that CRISPR systems are also encoded in diverse bacteriophages, where they occur as divergent and hypercompact anti-viral systems. Bacteriophage-encoded CRISPR systems belong to all six known CRISPR-Cas types, though some lack crucial components, suggesting alternate functional roles or host complementation. We describe multiple new Cas9-like proteins and 44 families related to type V CRISPR-Cas systems, including the Casλ RNA-guided nuclease family. Among the most divergent of the new enzymes identified, Casλ recognizes double-stranded DNA using a uniquely structured CRISPR RNA (crRNA). The Casλ-RNA-DNA structure determined by cryoelectron microscopy reveals a compact bilobed architecture capable of inducing genome editing in mammalian, Arabidopsis, and hexaploid wheat cells. These findings reveal a new source of CRISPR-Cas enzymes in phages and highlight their value as genome editors in plant and human cells. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27320.map.gz | 1.1 MB | EMDB map data format | |
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Header (meta data) | emd-27320-v30.xml emd-27320.xml | 23.3 KB 23.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27320_fsc.xml | 7.5 KB | Display | FSC data file |
Images | emd_27320.png | 84.4 KB | ||
Masks | emd_27320_msk_1.map | 30.5 MB | Mask map | |
Filedesc metadata | emd-27320.cif.gz | 6.6 KB | ||
Others | emd_27320_additional_1.map.gz emd_27320_additional_2.map.gz emd_27320_half_map_1.map.gz emd_27320_half_map_2.map.gz | 28.8 MB 15.4 MB 28.4 MB 28.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27320 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27320 | HTTPS FTP |
-Validation report
Summary document | emd_27320_validation.pdf.gz | 919.3 KB | Display | EMDB validaton report |
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Full document | emd_27320_full_validation.pdf.gz | 918.8 KB | Display | |
Data in XML | emd_27320_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | emd_27320_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27320 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27320 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27320.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | LocSpiral map from cryoSPARC half maps | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.115 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_27320_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: cryoSPARC sharp map
File | emd_27320_additional_1.map | ||||||||||||
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Annotation | cryoSPARC sharp map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: cryoSPARC map
File | emd_27320_additional_2.map | ||||||||||||
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Annotation | cryoSPARC map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27320_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27320_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CasLambda-crRNA-dsDNA ternary structure
Entire | Name: CasLambda-crRNA-dsDNA ternary structure |
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Components |
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-Supramolecule #1: CasLambda-crRNA-dsDNA ternary structure
Supramolecule | Name: CasLambda-crRNA-dsDNA ternary structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: uncultured virus (environmental samples) |
-Macromolecule #1: CasLambda
Macromolecule | Name: CasLambda / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: uncultured virus (environmental samples) |
Molecular weight | Theoretical: 87.337969 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MASHKKTESN QIIKTFSFKI KNANGLSLDV LNDAITEYQN YYNICSDWIK DHLTMKISEL YKYIPNEKKN SGYALTLISD EWKDKPMYM MFKKGYPANN RDNAIYETLN TCNTEHYTGN ILNFSDTYYR RFGYVASAIS NYVTKISKMS TGSRSKNISN D SDVDTIME ...String: MASHKKTESN QIIKTFSFKI KNANGLSLDV LNDAITEYQN YYNICSDWIK DHLTMKISEL YKYIPNEKKN SGYALTLISD EWKDKPMYM MFKKGYPANN RDNAIYETLN TCNTEHYTGN ILNFSDTYYR RFGYVASAIS NYVTKISKMS TGSRSKNISN D SDVDTIME QVIYEMEHNG WTSVKDWENQ MEYLESKTDS NPNFVYRMTT LYEFYKSHID EVNSKMETMS IDSLIKFGGC RR KDSKKSM YIMGGSNTPF DITQIGGNSL NIKFSKNLNV DVFGRYDVIK DNTLLVDIIN GHGASFVLKI INDEIYIDIN VSV PFDKKI ATTNKVVGID VNIKHMLLAT NILDDGNVKG YVNIYKEVIN DSDFKKVCNS TVMQYFTDFS KFVTFCPLEF DFLF SRVCN QKGIYNDNSA MEKSFSDVLN KLKWNFIETG DNTKRIYIEN VMKLRSQMKA YAIVKNAYYK QQSEYDFGKS EEFIQ EHPF SNTDKGIEIL NKLDNISKKI LGCRNNIIQY SYNLFEINGY DMVSLEKLTS SQFKKKPFPT VNSLLKYHKI LGCTQE EME KKDIYSVIKK GYYDIIFDND VVTDAKLSAK GELSKFKDDF FNLMIKSIHF ADIKDYFITL SNNGTAGVSL VPSYFTS QM DSIDHKIYFV QDNKSGKLKL ANKHKVRSSQ EKHINGLNAD YNAARNIAYI MENTDCRNMF MKQSRTDKSL YNKPSYET F IKTQGSAVAK LKKEGFVKIL DEASVGSSGH HHHHH |
-Macromolecule #2: RNA (51-MER)
Macromolecule | Name: RNA (51-MER) / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: uncultured virus (environmental samples) |
Molecular weight | Theoretical: 16.483719 KDa |
Sequence | String: AUUGUUGUAA CUCUUAUUUU GUAUGGAGUA AACAACUAGC AUCACCUUCA CC |
-Macromolecule #3: DNA TS
Macromolecule | Name: DNA TS / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: uncultured virus (environmental samples) |
Molecular weight | Theoretical: 14.296228 KDa |
Sequence | String: (DC)(DA)(DT)(DT)(DA)(DA)(DC)(DA)(DT)(DT) (DA)(DC)(DT)(DA)(DA)(DG)(DA)(DG)(DG)(DG) (DT)(DG)(DA)(DA)(DG)(DG)(DT)(DG)(DA) (DT)(DG)(DC)(DT)(DA)(DC)(DA)(DA)(DA)(DC) (DG) (DG)(DT)(DC)(DA)(DA)(DG) |
-Macromolecule #4: DNA NTS
Macromolecule | Name: DNA NTS / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: uncultured virus (environmental samples) |
Molecular weight | Theoretical: 14.371228 KDa |
Sequence | String: (DC)(DT)(DT)(DG)(DA)(DC)(DC)(DG)(DT)(DT) (DT)(DG)(DA)(DT)(DC)(DG)(DT)(DA)(DG)(DT) (DG)(DG)(DA)(DA)(DG)(DT)(DG)(DG)(DG) (DA)(DG)(DA)(DT)(DA)(DG)(DT)(DA)(DA)(DT) (DG) (DT)(DT)(DA)(DA)(DT)(DG) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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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: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | PDB-8dc2: |