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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Structure of CasPi with guide RNA and target DNA | |||||||||
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Function / homology | Reverse transcriptase domain-containing protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Li CP / Wang J / Liu JJ | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The compact Casπ (Cas12l) 'bracelet' provides a unique structural platform for DNA manipulation. Authors: Ao Sun / Cheng-Ping Li / Zhihang Chen / Shouyue Zhang / Dan-Yuan Li / Yun Yang / Long-Qi Li / Yuqian Zhao / Kaichen Wang / Zhaofu Li / Jinxia Liu / Sitong Liu / Jia Wang / Jun-Jie Gogo Liu / ![]() Abstract: CRISPR-Cas modules serve as the adaptive nucleic acid immune systems for prokaryotes, and provide versatile tools for nucleic acid manipulation in various organisms. Here, we discovered a new ...CRISPR-Cas modules serve as the adaptive nucleic acid immune systems for prokaryotes, and provide versatile tools for nucleic acid manipulation in various organisms. Here, we discovered a new miniature type V system, CRISPR-Casπ (Cas12l) (~860 aa), from the environmental metagenome. Complexed with a large guide RNA (~170 nt) comprising the tracrRNA and crRNA, Casπ (Cas12l) recognizes a unique 5' C-rich PAM for DNA cleavage under a broad range of biochemical conditions, and generates gene editing in mammalian cells. Cryo-EM study reveals a 'bracelet' architecture of Casπ effector encircling the DNA target at 3.4 Å resolution, substantially different from the canonical 'two-lobe' architectures of Cas12 and Cas9 nucleases. The large guide RNA serves as a 'two-arm' scaffold for effector assembly. Our study expands the knowledge of DNA targeting mechanisms by CRISPR effectors, and offers an efficient but compact platform for DNA manipulation. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 49.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.6 KB 19.6 KB | Display Display | ![]() |
Images | ![]() | 106.5 KB | ||
Others | ![]() ![]() | 49 MB 49 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yojMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 0.856 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33983_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33983_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : CasPi
Entire | Name: CasPi |
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Components |
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-Supramolecule #1: CasPi
Supramolecule | Name: CasPi / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 177.28 KDa |
-Macromolecule #1: CasPi
Macromolecule | Name: CasPi / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 98.731234 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MAKATKEVKS KRVEALRQVA YQRLERLERK AQKIGAHLRK PGKAADLQSL HYLLHKVEVE YHDIARNLEK DPTWTPKPKM RREKRAIVP ESGPAAPLPT TAKGEPGRPA NRHIPPPVPL DSARIPEDQQ SMGQGSGGRS WCSAPFVEVK LPPTQWSNVR E KLLKFRIE ...String: MAKATKEVKS KRVEALRQVA YQRLERLERK AQKIGAHLRK PGKAADLQSL HYLLHKVEVE YHDIARNLEK DPTWTPKPKM RREKRAIVP ESGPAAPLPT TAKGEPGRPA NRHIPPPVPL DSARIPEDQQ SMGQGSGGRS WCSAPFVEVK LPPTQWSNVR E KLLKFRIE DDADIVRRWA EAKFGSIETA RDGLRASAEI GTSPDVWRSF ISRAISNGKK DFEPLLSLDD DELTADATAE RV VRRWHQI DWVGRMLDSI LETVPSGVSK DTFRSRVESR LKTFHSSVNS FELKKRKDGT VERKRKHTNP QFPYLSPSAV SID PDVVTM EAVELLQMQP EERFAKDPND ANGRMRLRVL QAELGKARRE ALGRRGEKAP PWSGRKVFRG TTTRKREACL VWDK EAQAD GLYFALVMSG GPKIDDKRFV YMDGQPLQSD WQLHNGVAGK AKSCRAMPLI LKHDFLRWYH RHIKNHDVNA PLEKR CVHT TTQFVFVEPD EKKGLQPRLF IRPVFKFYDP VYEVPDSHSI DKKPDCRYLI GIARGVNYPY RAAVYDCETN SIIADK FVD GRKADWERIR NELAYHQRRR DLLRNSRASS AAIQREIRAI ARIRKRERGL NKVETVESIA RLVDWAEENL GKCNYCF VL ADLSSNLNLG RNNRVKHIAA IKEALINQMR KRGYRFKKSG KVDGVREESA WYTSAVAPSG WWAKKEEVDG AWKADKTR P LARKIGSYYC CEEIDGLHLR GVLKGLGRAK RLVLQSDDPS APTRRRGFGS ELFWDPYCTE LCGHAFPQGV VLDADFIGA FNIALRPLVR EELGKKAKAV DLADRHQTLN PTVALRCGVT AYEFVEVGGD PRGGLRKILL NPAEAVI |
-Macromolecule #2: DNA (5'-D(P*CP*GP*GP*GP*AP*TP*GP*CP*CP*CP*AP*G)-3')
Macromolecule | Name: DNA (5'-D(P*CP*GP*GP*GP*AP*TP*GP*CP*CP*CP*AP*G)-3') / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 3.688405 KDa |
Sequence | String: (DC)(DG)(DG)(DG)(DA)(DT)(DG)(DC)(DC)(DC) (DA)(DG) |
-Macromolecule #3: DNA (30-MER)
Macromolecule | Name: DNA (30-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 9.192878 KDa |
Sequence | String: (DG)(DT)(DT)(DC)(DA)(DC)(DC)(DA)(DG)(DG) (DG)(DT)(DG)(DT)(DC)(DG)(DC)(DC)(DC)(DT) (DG)(DG)(DG)(DC)(DA)(DT)(DC)(DC)(DC) (DG) |
-Macromolecule #4: RNA (174-MER)
Macromolecule | Name: RNA (174-MER) / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 56.411703 KDa |
Sequence | String: GUCUGCCGAA GACGCCGCAC GGAGCCUGGG CCGGAAUCGU AGAUCGAACG CGGCAUCGAA GCCCUGCAGC CCUUCGGGGC CAAGGCGGC GCAGCAAGCC UCUUUCAGGC GGCAGAGUCC UUUAGAGUGU GAGAGACACU CUAAAGGAAU GAAAGAGGGC G ACACCCUG GUGAAC |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing #1
Startup model | Type of model: NONE / Details: ab-initial in cryosparc |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final 3D classification | Number classes: 3 |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39500 |
Image processing ID | 1 |
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Image processing #2
Startup model | Type of model: NONE / Details: ab-initial in cryosparc |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final 3D classification | Number classes: 3 |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39500 |
Image processing ID | 2 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: BACKBONE TRACE |
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Output model | ![]() PDB-7yoj: |