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Yorodumi- EMDB-21516: Cryo-EM structure of anti-CRISPR AcrIF9, bound to the type I-F cr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21516 | ||||||||||||
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Title | Cryo-EM structure of anti-CRISPR AcrIF9, bound to the type I-F crRNA-guided CRISPR surveillance complex | ||||||||||||
Map data | anti-CRISPR AcrIF9 bound to the type I-F crRNA-guided CRISPR surveillance complex | ||||||||||||
Sample |
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Keywords | type I-F CRISPR RNA-guided surveillance complex / Csy complex / IMMUNE SYSTEM-RNA complex | ||||||||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding Similarity search - Function | ||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) / Proteus penneri (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Hirschi M / Santiago-Frangos A | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Commun / Year: 2020 Title: AcrIF9 tethers non-sequence specific dsDNA to the CRISPR RNA-guided surveillance complex. Authors: Marscha Hirschi / Wang-Ting Lu / Andrew Santiago-Frangos / Royce Wilkinson / Sarah M Golden / Alan R Davidson / Gabriel C Lander / Blake Wiedenheft / Abstract: Bacteria have evolved sophisticated adaptive immune systems, called CRISPR-Cas, that provide sequence-specific protection against phage infection. In turn, phages have evolved a broad spectrum of ...Bacteria have evolved sophisticated adaptive immune systems, called CRISPR-Cas, that provide sequence-specific protection against phage infection. In turn, phages have evolved a broad spectrum of anti-CRISPRs that suppress these immune systems. Here we report structures of anti-CRISPR protein IF9 (AcrIF9) in complex with the type I-F CRISPR RNA-guided surveillance complex (Csy). In addition to sterically blocking the hybridization of complementary dsDNA to the CRISPR RNA, our results show that AcrIF9 binding also promotes non-sequence-specific engagement with dsDNA, potentially sequestering the complex from target DNA. These findings highlight the versatility of anti-CRISPR mechanisms utilized by phages to suppress CRISPR-mediated immune systems. | ||||||||||||
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_21516.map.gz | 28.6 MB | EMDB map data format | |
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Header (meta data) | emd-21516-v30.xml emd-21516.xml | 20.3 KB 20.3 KB | Display Display | EMDB header |
Images | emd_21516.png | 211.3 KB | ||
Filedesc metadata | emd-21516.cif.gz | 6.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21516 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21516 | HTTPS FTP |
-Validation report
Summary document | emd_21516_validation.pdf.gz | 555.8 KB | Display | EMDB validaton report |
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Full document | emd_21516_full_validation.pdf.gz | 555.4 KB | Display | |
Data in XML | emd_21516_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | emd_21516_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21516 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21516 | HTTPS FTP |
-Related structure data
Related structure data | 6w1xMC 6whiC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21516.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | anti-CRISPR AcrIF9 bound to the type I-F crRNA-guided CRISPR surveillance complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 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 : Anti-CRISPR AcrIF9 bound to the type I-F crRNA-guided CRISPR surv...
Entire | Name: Anti-CRISPR AcrIF9 bound to the type I-F crRNA-guided CRISPR surveillance complex |
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Components |
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-Supramolecule #1: Anti-CRISPR AcrIF9 bound to the type I-F crRNA-guided CRISPR surv...
Supramolecule | Name: Anti-CRISPR AcrIF9 bound to the type I-F crRNA-guided CRISPR surveillance complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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-Supramolecule #2: Type I-F crRNA-guided CRISPR surveillance complex
Supramolecule | Name: Type I-F crRNA-guided CRISPR surveillance complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
-Supramolecule #3: Anti-CRISPR AcrIF9
Supramolecule | Name: Anti-CRISPR AcrIF9 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6 |
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Source (natural) | Organism: Proteus penneri (bacteria) |
-Macromolecule #1: CRISPR-associated protein Csy1
Macromolecule | Name: CRISPR-associated protein Csy1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Molecular weight | Theoretical: 49.194168 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTSPLPTPTW QELRQFIESF IQERLQGKLD KLQPDEDDKR QTLLATHRRE AWLADAARRV GQLQLVTHTL KPIHPDARGS NLHSLPQAP GQPGLAGSHE LGDRLVSDVV GNAAALDVFK FLSLQYQGKN LLNWLTEDSA EALQALSDNA EQAREWRQAF I GITTVKGA ...String: MTSPLPTPTW QELRQFIESF IQERLQGKLD KLQPDEDDKR QTLLATHRRE AWLADAARRV GQLQLVTHTL KPIHPDARGS NLHSLPQAP GQPGLAGSHE LGDRLVSDVV GNAAALDVFK FLSLQYQGKN LLNWLTEDSA EALQALSDNA EQAREWRQAF I GITTVKGA PASHSLAKQL YFPLPGSGYH LLAPLFPTSL VHHVHALLRE ARFGDAAKAA REARSRQESW PHGFSEYPNL AI QKFGGTK PQNISQLNNE RRGENWLLPS LPPNWQRQNV NAPMRHSSVF EHDFGRTPEV SRLTRTLQRF LAKTVHNNLA IRQ RRAQLV AQICDEALQY AARLRELEPG WSATPGCQLH DAEQLWLDPL RAQTDETFLQ RRLRGDWPAE VGNRFANWLN RAVS SDSQI LGSPEAAQWS QELSKELTMF KEILEDERD UniProtKB: CRISPR-associated protein Csy1 |
-Macromolecule #2: Type I-F CRISPR-associated protein Csy2
Macromolecule | Name: Type I-F CRISPR-associated protein Csy2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Molecular weight | Theoretical: 36.244074 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSVTDPEALL LLPRLSIQNA NAISSPLTWG FPSPGAFTGF VHALQRRVGI SLDIELDGVG IVCHRFEAQI SQPAGKRTKV FNLTRNPLN RDGSTAAIVE EGRAHLEVSL LLGVHGDGLD DHPAQEIARQ VQEQAGAMRL AGGSILPWCN ERFPAPNAEL L MLGGSDEQ ...String: MSVTDPEALL LLPRLSIQNA NAISSPLTWG FPSPGAFTGF VHALQRRVGI SLDIELDGVG IVCHRFEAQI SQPAGKRTKV FNLTRNPLN RDGSTAAIVE EGRAHLEVSL LLGVHGDGLD DHPAQEIARQ VQEQAGAMRL AGGSILPWCN ERFPAPNAEL L MLGGSDEQ RRKNQRRLTR RLLPGFALVS REALLQQHLE TLRTTLPEAT TLDALLDLCR INFEPPATSS EEEASPPDAA WQ VRDKPGW LVPIPAGYNA LSPLYLPGEV RNARDRETPL RFVENLFGLG EWLSPHRVAA LSDLLWYHHA EPDKGLYRWS TPR FVEHAI A UniProtKB: Uncharacterized protein |
-Macromolecule #3: CRISPR-associated protein Csy3
Macromolecule | Name: CRISPR-associated protein Csy3 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Molecular weight | Theoretical: 39.778594 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKSSHHHHHH ENLYFQSNAS KPILSTASVL AFERKLDPSD ALMSAGAWAQ RDASQEWPAV TVREKSVRGT ISNRLKTKDR DPAKLDASI QSPNLQTVDV ANLPSDADTL KVRFTLRVLG GAGTPSACND AAYRDKLLQT VATYVNDQGF AELARRYAHN L ANARFLWR ...String: MKSSHHHHHH ENLYFQSNAS KPILSTASVL AFERKLDPSD ALMSAGAWAQ RDASQEWPAV TVREKSVRGT ISNRLKTKDR DPAKLDASI QSPNLQTVDV ANLPSDADTL KVRFTLRVLG GAGTPSACND AAYRDKLLQT VATYVNDQGF AELARRYAHN L ANARFLWR NRVGAEAVEV RINHIRQGEV ARAWRFDALA IGLRDFKADA ELDALAELIA SGLSGSGHVL LEVVAFARIG DG QEVFPSQ ELILDKGDKK GQKSKTLYSV RDAAAIHSQK IGNALRTIDT WYPDEDGLGP IAVEPYGSVT SQGKAYRQPK QKL DFYTLL DNWVLRDEAP AVEQQHYVIA NLIRGGVFGE AEEK UniProtKB: CRISPR type I-F/YPEST-associated protein Csy3 |
-Macromolecule #5: CRISPR-associated endonuclease Cas6/Csy4
Macromolecule | Name: CRISPR-associated endonuclease Cas6/Csy4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Molecular weight | Theoretical: 21.427504 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDHYLDIRLR PDPEFPPAQL MSVLFGKLHQ ALVAQGGDRI GVSFPDLDES RSRLGERLRI HASADDLRAL LARPWLEGLR DHLQFGEPA VVPHPTPYRQ VSRVQAKSNP ERLRRRLMRR HDLSEEEARK RIPDTVARAL DLPFVTLRSQ STGQHFRLFI R HGPLQVTA EEGGFTCYGL SKGGFVPWF UniProtKB: CRISPR-associated endonuclease Cas6/Csy4 |
-Macromolecule #6: anti-CRISPR AcrIF9
Macromolecule | Name: anti-CRISPR AcrIF9 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Proteus penneri (bacteria) |
Molecular weight | Theoretical: 7.863849 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKSTYIIKEV QNINSDREGV KVETTSLTSA KRIASKNQFF HGTVLRIESE SGNWLAYKED GKRWIECE UniProtKB: SH3b domain-containing protein |
-Macromolecule #4: RNA (60-MER)
Macromolecule | Name: RNA (60-MER) / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Molecular weight | Theoretical: 19.265404 KDa |
Sequence | String: CUAAGAAAUU CACGGCGGGC UUGAUGUCCG CGUCUACCUG GUUCACUGCC GUGUAGGCAG GENBANK: GENBANK: HQ326201.1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL | ||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER / Details: unspecified | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1653 / Average exposure time: 13.2 sec. / Average electron dose: 66.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 36000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |