+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21366 | |||||||||
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Title | Cryo-EM structure of AcrVIA1-Cas13(crRNA) complex | |||||||||
Map data | AcrVIA1-Cas13(crRNA) complex | |||||||||
Sample |
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Keywords | CRISPR-Cas system / Cas13 / type VIA / IMMUNE SYSTEM / Anti-CRISPR / HYDROLASE / RNA | |||||||||
Function / homology | : / defense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / RNA binding / CRISPR-associated endoribonuclease Cas13a Function and homology information | |||||||||
Biological species | Listeria seeligeri (bacteria) / Listeria seeligeri serovar 1/2b str. SLCC3954 (bacteria) / Listeria seeligeri serovar 1/2b (strain ATCC 35967 / DSM 20751 / CIP 100100 / SLCC 3954) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Jia N / Meeske AJ | |||||||||
Citation | Journal: Science / Year: 2020 Title: A phage-encoded anti-CRISPR enables complete evasion of type VI-A CRISPR-Cas immunity. Authors: Alexander J Meeske / Ning Jia / Alice K Cassel / Albina Kozlova / Jingqiu Liao / Martin Wiedmann / Dinshaw J Patel / Luciano A Marraffini / Abstract: The CRISPR RNA (crRNA)-guided nuclease Cas13 recognizes complementary viral transcripts to trigger the degradation of both host and viral RNA during the type VI CRISPR-Cas antiviral response. ...The CRISPR RNA (crRNA)-guided nuclease Cas13 recognizes complementary viral transcripts to trigger the degradation of both host and viral RNA during the type VI CRISPR-Cas antiviral response. However, how viruses can counteract this immunity is not known. We describe a listeriaphage (ϕLS46) encoding an anti-CRISPR protein (AcrVIA1) that inactivates the type VI-A CRISPR system of Using genetics, biochemistry, and structural biology, we found that AcrVIA1 interacts with the guide-exposed face of Cas13a, preventing access to the target RNA and the conformational changes required for nuclease activation. Unlike inhibitors of DNA-cleaving Cas nucleases, which cause limited immunosuppression and require multiple infections to bypass CRISPR defenses, a single dose of AcrVIA1 delivered by an individual virion completely dismantles type VI-A CRISPR-mediated immunity. | |||||||||
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_21366.map.gz | 2.9 MB | EMDB map data format | |
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Header (meta data) | emd-21366-v30.xml emd-21366.xml | 11.8 KB 11.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21366_fsc.xml | 7 KB | Display | FSC data file |
Images | emd_21366.png | 90 KB | ||
Filedesc metadata | emd-21366.cif.gz | 6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21366 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21366 | HTTPS FTP |
-Validation report
Summary document | emd_21366_validation.pdf.gz | 401.5 KB | Display | EMDB validaton report |
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Full document | emd_21366_full_validation.pdf.gz | 401.1 KB | Display | |
Data in XML | emd_21366_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | emd_21366_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21366 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21366 | HTTPS FTP |
-Related structure data
Related structure data | 6vrbMC 6vrcC 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_21366.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | AcrVIA1-Cas13(crRNA) complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 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 : Cas13-crRNA-AcrVIA1 complex
Entire | Name: Cas13-crRNA-AcrVIA1 complex |
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Components |
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-Supramolecule #1: Cas13-crRNA-AcrVIA1 complex
Supramolecule | Name: Cas13-crRNA-AcrVIA1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Listeria seeligeri (bacteria) |
-Macromolecule #1: RNA (52-MER)
Macromolecule | Name: RNA (52-MER) / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: Listeria seeligeri serovar 1/2b str. SLCC3954 (bacteria) |
Molecular weight | Theoretical: 16.534871 KDa |
Sequence | String: GACUACCUCU AUAUGAAAGA GGACUAAAAC CAUAUUUCCA AACUCCACUU UG GENBANK: GENBANK: FN557490.1 |
-Macromolecule #2: CRISPR-associated endoribonuclease Cas13a
Macromolecule | Name: CRISPR-associated endoribonuclease Cas13a / 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: Listeria seeligeri serovar 1/2b (strain ATCC 35967 / DSM 20751 / CIP 100100 / SLCC 3954) (bacteria) Strain: ATCC 35967 / DSM 20751 / CIP 100100 / SLCC 3954 |
Molecular weight | Theoretical: 128.350414 KDa |
Recombinant expression | Organism: Listeria seeligeri (bacteria) |
Sequence | String: TMRITKVEVD RKKVLISRDK NGGKLVYENE MQDNTEQIMH HKKSSFYKSV VNKTICRPEQ KQMKKLVHGL LQENSQEKIK VSDVTKLNI SNFLNHRFKK SLYYFPENSP DKSEEYRIEI NLSQLLEDSL KKQQGTFICW ESFSKDMELY INWAENYISS K TKLIKKSI ...String: TMRITKVEVD RKKVLISRDK NGGKLVYENE MQDNTEQIMH HKKSSFYKSV VNKTICRPEQ KQMKKLVHGL LQENSQEKIK VSDVTKLNI SNFLNHRFKK SLYYFPENSP DKSEEYRIEI NLSQLLEDSL KKQQGTFICW ESFSKDMELY INWAENYISS K TKLIKKSI RNNRIQSTES RSGQLMDRYM KDILNKNKPF DIQSVSEKYQ LEKLTSALKA TFKEAKKNDK EINYKLKSTL QN HERQIIE ELKENSELNQ FNIEIRKHLE TYFPIKKTNR KVGDIRNLEI GEIQKIVNHR LKNKIVQRIL QEGKLASYEI EST VNSNSL QKIKIEEAFA LKFINACLFA SNNLRNMVYP VCKKDILMIG EFKNSFKEIK HKKFIRQWSQ FFSQEITVDD IELA SWGLR GAIAPIRNEI IHLKKHSWKK FFNNPTFKVK KSKIINGKTK DVTSEFLYKE TLFKDYFYSE LDSVPELIIN KMESS KILD YYSSDQLNQV FTIPNFELSL LTSAVPFAPS FKRVYLKGFD YQNQDEAQPD YNLKLNIYNE KAFNSEAFQA QYSLFK MVY YQVFLPQFTT NNDLFKSSVD FILTLNKERK GYAKAFQDIR KMNKDEKPSE YMSYIQSQLM LYQKKQEEKE KINHFEK FI NQVFIKGFNS FIEKNRLTYI CHPTKNTVPE NDNIEIPFHT DMDDSNIAFW LMCKLLDAKQ LSELRNEMIK FSCSLQST E EISTFTKARE VIGLALLNGE KGCNDWKELF DDKEAWKKNM SLYVSEELLQ SLPYTQEDGQ TPVINRSIDL VKKYGTETI LEKLFSSSDD YKVSAKDIAK LHEYDVTEKI AQQESLHKQW IEKPGLARDS AWTKKYQNVI NDISNYQWAK TKVELTQVRH LHQLTIDLL SRLAGYMSIA DRDFQFSSNY ILERENSEYR VTSWILLSEN KNKNKYNDYE LYNLKNASIK VSSKNDPQLK V DLKQLRLT LEYLELFDNR LKEKRNNISH FNYLNGQLGN SILELFDDAR DVLSYDRKLK NAVSKSLKEI LSSHGMEVTF KP LYQTNHH LKIDKLQPKK IHHLGEKSTV SSNQVSNEYC QLVRTLLTMK UniProtKB: CRISPR-associated endoribonuclease Cas13a |
-Macromolecule #3: AcrVIA1
Macromolecule | Name: AcrVIA1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Listeria seeligeri (bacteria) |
Molecular weight | Theoretical: 27.144854 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MIYYIKDLKV KGKIFENLMN KEAVEGLITF LKKAEFEIYS RENYSKYNKW FEMWKSPTSS LVFWKNYSFR CHLLFVIEKD GECLGIPAS VFESVLQIYL ADPFAPDTKE LFVEVCNLYE CLADVTVVEH FEAEESAWHK LTHNETEVSK RVYSKDDDEL L KYIPEFLD ...String: MIYYIKDLKV KGKIFENLMN KEAVEGLITF LKKAEFEIYS RENYSKYNKW FEMWKSPTSS LVFWKNYSFR CHLLFVIEKD GECLGIPAS VFESVLQIYL ADPFAPDTKE LFVEVCNLYE CLADVTVVEH FEAEESAWHK LTHNETEVSK RVYSKDDDEL L KYIPEFLD TIATNKKSQK YNQIQGKIQE INKEIATLYE SSEDYIFTEY VSNLYRESAK LEQHSKQILK E |
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.23 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |