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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Type I-EHNH Cascade complex | |||||||||
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![]() | RNA pro / RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | ![]() maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA binding / zinc ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.06 Å | |||||||||
![]() | Li Z | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Mechanisms for HNH-mediated target DNA cleavage in type I CRISPR-Cas systems. Authors: Chendi Zhang / Fugen Chen / Feng Wang / Haijiang Xu / Jialin Xue / Zhuang Li / ![]() Abstract: The metagenome-derived type I-E and type I-F variant CRISPR-associated complex for antiviral defense (Cascade) complexes, fused with HNH domains, precisely cleave target DNA, representing recently ...The metagenome-derived type I-E and type I-F variant CRISPR-associated complex for antiviral defense (Cascade) complexes, fused with HNH domains, precisely cleave target DNA, representing recently identified genome editing tools. However, the underlying working mechanisms remain unknown. Here, structures of type I-F and I-E Cascade complexes at different states are reported. In type I-F Cascade, Cas8f loosely attaches to Cascade head and is adjacent to the 5' end of the target single-stranded DNA (ssDNA). Formation of the full R-loop drives the Cascade head to move outward, allowing Cas8f to detach and rotate ∼150° to accommodate target ssDNA for cleavage. In type I-E Cascade, Cas5e domain is adjacent to the 5' end of the target ssDNA. Full crRNA-target pairing drives the lift of the Cascade head, widening the substrate channel for target ssDNA entrance. Altogether, these analyses into both complexes revealed that crRNA-guided positioning of target DNA and target DNA-induced HNH unlocking are two key factors for their site-specific cleavage of target DNA. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 117.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.7 KB 19.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 105.4 KB | ||
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() | 115.9 MB 115.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8yb6MC ![]() 8ydbC ![]() 8yeoC ![]() 8yh9C ![]() 8yhaC 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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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_39110_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_39110_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Type I-EHNH Cascade complex
Entire | Name: Type I-EHNH Cascade complex |
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Components |
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-Supramolecule #1: Type I-EHNH Cascade complex
Supramolecule | Name: Type I-EHNH Cascade complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: CRISPR system Cascade subunit CasD
Macromolecule | Name: CRISPR system Cascade subunit CasD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 43.621383 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSAPPNTLFL RLEGALQSWG SNEAKFALRR TADAPTKSGV LGLLCAAMGI GRAEAADSWL PKLANLRMGV RIDRPGIRWW DFHTVGAGQ RMRMAELKAP KKPSMVGAAL AETLTPSKVK TRAETLLSRR EYLADASFLV ALQGEPELVA KLSAALAKPV W AIYLGRKS ...String: MSAPPNTLFL RLEGALQSWG SNEAKFALRR TADAPTKSGV LGLLCAAMGI GRAEAADSWL PKLANLRMGV RIDRPGIRWW DFHTVGAGQ RMRMAELKAP KKPSMVGAAL AETLTPSKVK TRAETLLSRR EYLADASFLV ALQGEPELVA KLSAALAKPV W AIYLGRKS CPPSRPVCEH PPGFYNTLEE ALSAVPLQKR WHNEPLPQIL PCVMDWIPGY DGEHAPDDAE IHYDLPVSFQ PP RHLPRFV IRRELVVGED VQVSRETGTS VWRPKGTRAD YNNSEYKKVR AERLVMDHAA CMVCKAPATT VQHVNYRRAG GKE IPEDLR ALCRLCHDAC TMLEYGSGMT TNRIDPCDPI WRERILAKRK EIVEFRSRGQ RFRKMKPEEE NG UniProtKB: CRISPR system Cascade subunit CasD |
-Macromolecule #2: CRISPR-associated endoribonuclease Cse3
Macromolecule | Name: CRISPR-associated endoribonuclease Cse3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 31.218768 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MIYLSRLLID TGGNPDRPRP GRKWLDNIYN VHRRLSMAFP SGLRREQDPH FLKPFSPNDF QKTPFLFRVD NNIDGNDKRA IIIVQSVLE PDWDYCFQNA LDFLAAPPET KEYNPEFKAG QLLRFRLRVN ASVRRHIPEM VQQDGQTIET GKILHKRVSL T WDASSTPD ...String: MIYLSRLLID TGGNPDRPRP GRKWLDNIYN VHRRLSMAFP SGLRREQDPH FLKPFSPNDF QKTPFLFRVD NNIDGNDKRA IIIVQSVLE PDWDYCFQNA LDFLAAPPET KEYNPEFKAG QLLRFRLRVN ASVRRHIPEM VQQDGQTIET GKILHKRVSL T WDASSTPD QALADWLAAK SPKLGFTLQR CELLQLGWVY GSKPEPKNVK VKEQGQGYWR EHKYNPLRFR AALLEGVLEV DD PKLFLKT LSSGIGKAKS FGFGLLSVLP IRNDG UniProtKB: CRISPR-associated endoribonuclease Cse3 |
-Macromolecule #4: CRISPR system Cascade subunit CasC
Macromolecule | Name: CRISPR system Cascade subunit CasC / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 41.794367 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MLIEIHMIQN HSPANLNRDD LGAPKTCYFG GVLRSRISSQ CIKRSIRTSN DFKALLGGVR TRRLADLIQQ EAGETECWKK AQEILNKCG FKNKDDNTKM LVFMSKDKIK DLARIVLDNS LGLTEAAQQV ANVIAQATLA PDIALCGRML EPNDKDKDKK V KWSNTTVE ...String: MLIEIHMIQN HSPANLNRDD LGAPKTCYFG GVLRSRISSQ CIKRSIRTSN DFKALLGGVR TRRLADLIQQ EAGETECWKK AQEILNKCG FKNKDDNTKM LVFMSKDKIK DLARIVLDNS LGLTEAAQQV ANVIAQATLA PDIALCGRML EPNDKDKDKK V KWSNTTVE AALQVAHAIS THIARPEIDY FVAADDVPGE DAGAGHIGES MFASACFYKY FSIDWEQLVK NLKGDTNLAA HT VGAFLLA AAKTNPSGKQ NSFAAHNYPD GILVEFKNSP ISYANAFVRP VSVVKESDLV EQSIGQLSNY VNDIRLGYYD EQS PVIGFW FSPNNRYPLG YKHSKLASRN IGNLNELVGA VLDYIGGFKW EEVQKSKAYI GG UniProtKB: CRISPR system Cascade subunit CasC |
-Macromolecule #5: CRISPR-associated protein Cse1 (CRISPR_cse1)
Macromolecule | Name: CRISPR-associated protein Cse1 (CRISPR_cse1) / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 60.665359 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MYCAAVCFPQ TKYQQRGTAL KKPLVGLRKM GVEAAAWNTL KVTRDRPKLT FPDLITPQSK FLDNDLWLKY KVPIEQKEHV MYNLLCDNW VNVVYLSGKP DRISLVQTLK DAHCLQLAYS NPMDRFTVFR FLLALGYWCF ANTNVEPEPD KPLPVSWIPW L EENKEYFE ...String: MYCAAVCFPQ TKYQQRGTAL KKPLVGLRKM GVEAAAWNTL KVTRDRPKLT FPDLITPQSK FLDNDLWLKY KVPIEQKEHV MYNLLCDNW VNVVYLSGKP DRISLVQTLK DAHCLQLAYS NPMDRFTVFR FLLALGYWCF ANTNVEPEPD KPLPVSWIPW L EENKEYFE LFGDGKRFFQ ADPSSRIRAI TDLIHEIPTA HNLCHFKHVT DYIDGLCEAC CIKGLLRLPV FTTVGGRGIG AG INNTPPF YLLWHANDLA GMLAQNWQPW DNMGIPAWLG SFQKESREVG LLAGMTWLPR KVYLHDPVPG QAACCSCGLP SEA LVYSCS IEVEPVPKGL EWKDPHGVYT DQGKSLQSKI KLMSNDRYTF ADRDWYSPLF SYLHAEGNSR QGKLWLVGFA SDKA KSIDI WDKIIELEGT DTNDELLAQL ANRATALNAM RKKPLRGDFK KSVGTPQIAD IIPHAENRIA INAGKMTENR GYSWQ DADT EYGELLTKVA YSLEPAQTVD ARLKRGNFIS RKPWPIIPES KTKPAEGDQN E UniProtKB: CRISPR-associated protein Cse1 (CRISPR_cse1) |
-Macromolecule #6: CRISPR-associated protein Cse2 (CRISPR_cse2)
Macromolecule | Name: CRISPR-associated protein Cse2 (CRISPR_cse2) / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 20.300639 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MNRGTVDFIA SLENLKEGDL GILRKLRGAR LDEKLPGFDL FSALWWPLRQ KNQRAPKREV AWLIAKLFAE FRFEQREGAT LPILMGGIC RKLEPKKELP RVLARFDQLA SLDIMQMEEP LSVIMGILRK HQQVCLDWVG LTDVLSFWEQ EPVKREWSDS F IKAYKINK EDSDVD UniProtKB: CRISPR-associated protein Cse2 (CRISPR_cse2) |
-Macromolecule #3: 61-nt crRNA
Macromolecule | Name: 61-nt crRNA / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 19.681744 KDa |
Sequence | String: GUGAACCGGA GAAGUCAUUU AAUAAGGCCA CUGUUAAAAA GUAUUCCCCA CGCAUGUGGG G |
-Macromolecule #7: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 7 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 6.2 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |