+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31185 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Csy-AcrIF24 | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | complex / inhibitor / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA complex | |||||||||
Function / homology | CRISPR-associated protein Csy1 / CRISPR-associated protein (Cas_Csy1) / CRISPR-associated protein Csy2 / CRISPR-associated protein (Cas_Csy2) / CRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3) / Uncharacterized protein / CRISPR-associated protein Csy3 / Uncharacterized protein Function and homology information | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.88 Å | |||||||||
Authors | Zhang L / Feng Y | |||||||||
Funding support | China, 1 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24. Authors: Lingguang Yang / Laixing Zhang / Peipei Yin / Hao Ding / Yu Xiao / Jianwei Zeng / Wenhe Wang / Huan Zhou / Qisheng Wang / Yi Zhang / Zeliang Chen / Maojun Yang / Yue Feng / Abstract: CRISPR-Cas systems are prokaryotic adaptive immune systems and phages use anti-CRISPR proteins (Acrs) to counteract these systems. Here, we report the structures of AcrIF24 and its complex with the ...CRISPR-Cas systems are prokaryotic adaptive immune systems and phages use anti-CRISPR proteins (Acrs) to counteract these systems. Here, we report the structures of AcrIF24 and its complex with the crRNA-guided surveillance (Csy) complex. The HTH motif of AcrIF24 can bind the Acr promoter region and repress its transcription, suggesting its role as an Aca gene in self-regulation. AcrIF24 forms a homodimer and further induces dimerization of the Csy complex. Apart from blocking the hybridization of target DNA to the crRNA, AcrIF24 also induces the binding of non-sequence-specific dsDNA to the Csy complex, similar to AcrIF9, although this binding seems to play a minor role in AcrIF24 inhibitory capacity. Further structural and biochemical studies of the Csy-AcrIF24-dsDNA complexes and of AcrIF24 mutants reveal that the HTH motif of AcrIF24 and the PAM recognition loop of the Csy complex are structural elements essential for this non-specific dsDNA binding. Moreover, AcrIF24 and AcrIF9 display distinct characteristics in inducing non-specific DNA binding. Together, our findings highlight a multifunctional Acr and suggest potential wide distribution of Acr-induced non-specific DNA binding. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_31185.map.gz | 7.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-31185-v30.xml emd-31185.xml | 15 KB 15 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_31185_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_31185.png | 221.1 KB | ||
Filedesc metadata | emd-31185.cif.gz | 6.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31185 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31185 | HTTPS FTP |
-Validation report
Summary document | emd_31185_validation.pdf.gz | 435.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_31185_full_validation.pdf.gz | 434.6 KB | Display | |
Data in XML | emd_31185_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | emd_31185_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31185 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31185 | HTTPS FTP |
-Related structure data
Related structure data | 7elmMC 7dtrC 7elnC 7we6C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_31185.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0742 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
-Entire : Csy-AcrIF24
Entire | Name: Csy-AcrIF24 |
---|---|
Components |
|
-Supramolecule #1: Csy-AcrIF24
Supramolecule | Name: Csy-AcrIF24 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
-Macromolecule #1: Type I-F CRISPR-associated protein Csy1
Macromolecule | Name: Type I-F CRISPR-associated protein Csy1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Molecular weight | Theoretical: 49.313254 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTSPLPTPTW QELRQFIESF IQERLQGKLD KLHPDEDDKR QTLLATHRRE AWLADAARRV GQLQLVTHTL KPIHPDARGS NLHSLPQAP GQPGLAGSHE LGDRLVSDVV GNAAALDVFK FLSLQYQGKN LLNWLTEDSA EAVQALSDNA EQAREWRQAF I GITAVKGA ...String: MTSPLPTPTW QELRQFIESF IQERLQGKLD KLHPDEDDKR QTLLATHRRE AWLADAARRV GQLQLVTHTL KPIHPDARGS NLHSLPQAP GQPGLAGSHE LGDRLVSDVV GNAAALDVFK FLSLQYQGKN LLNWLTEDSA EAVQALSDNA EQAREWRQAF I GITAVKGA PASHSLAKQL YFPLPGSGYH LLAPLFPTSL VHHVHALLRE ARFGDAAKAA REARSRQESW PHGFSEYPNL AI QKFGGTK PQNISQLNSE RYGENWLLPS LPPHWQRQDQ RAPIRHSSVF EHDFGRSPEV SRLTRTLQRL LAKTRHNNFT IRR YRAQLV GQICDEALQY AARLRELEPG WSATPGCQLH DAEQLWLDPL RAQTDETFLQ RRLRGDWPAE VGNRFANWLN RAVS SDSQI LGSPEAAQWS QELSKELTMF KEILEDERD UniProtKB: Uncharacterized protein |
-Macromolecule #2: CRISPR type I-F/YPEST-associated protein Csy2
Macromolecule | Name: CRISPR type I-F/YPEST-associated protein Csy2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
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: 12 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Molecular weight | Theoretical: 37.623324 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSKPILSTAS VLAFERKLDP SDALMSAGAW AQRDASQEWP AVTVREKSVR GTISNRLKTK DRDPAKLDAS IQSPNLQTVD VANLPSDAD TLKVRFTLRV LGGAGTPSAC NDAAYRDKLL QTVATYVNEQ GFAELARRYA HNLANARFLW RNRVGAEAVE V RINHIRQG ...String: MSKPILSTAS VLAFERKLDP SDALMSAGAW AQRDASQEWP AVTVREKSVR GTISNRLKTK DRDPAKLDAS IQSPNLQTVD VANLPSDAD TLKVRFTLRV LGGAGTPSAC NDAAYRDKLL QTVATYVNEQ GFAELARRYA HNLANARFLW RNRVGAEAVE V RINHIRQG EVARTWRFDA LAIGLRDFKA DAELDALAEL IASGLSGSGH VLLEVVAFAR IGDGQEVFPS QELILDKGDK KG QKSKTLY SVRDAAAIHS QKIGNALRTI DTWYPDEDGL GPIAVEPYGS VTSQGKAYRQ PKQKLDFYTL LDNWVLRDEA PAV EQQHYV IANLIRGGVF GEAEEK UniProtKB: CRISPR-associated protein Csy3 |
-Macromolecule #4: type I-F CRISPR-associated endoribonuclease Cas6/Csy4
Macromolecule | Name: type I-F CRISPR-associated endoribonuclease Cas6/Csy4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Molecular weight | Theoretical: 21.429477 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDHYLDIRLR PDPEFPPAQL MSVLFGKLHQ ALVAQGGDRI GVSFPDLDES RSRLGERLRI HASADDLRAL LARPWLEGLR DHLQFGEPA VVPHPTPYRQ VSRVQAKSNP ERLRRRLMRR HDLSEEEARK RIPDTVARTL DLPFVTLRSQ STGQHFRLFI R HGPLQATA EEGGFTCYGL SKGGFVPWF |
-Macromolecule #5: AcrIF24
Macromolecule | Name: AcrIF24 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Molecular weight | Theoretical: 24.995271 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MNAIHIGPFS ITPAARGLHY GGLPHHQWTL YYGPREMAIK TLPDSYTSSE VRDEFSDIIA EFVIDARHRY APDVLELVNS DGDAVLARV AVSRLPEALS GCIPDDRFPY WLLTASRPRL GLPVTLNEYT ALAVELSAPP LAWITGLLPG EVLTHDAEEW R PPTSWELR ...String: MNAIHIGPFS ITPAARGLHY GGLPHHQWTL YYGPREMAIK TLPDSYTSSE VRDEFSDIIA EFVIDARHRY APDVLELVNS DGDAVLARV AVSRLPEALS GCIPDDRFPY WLLTASRPRL GLPVTLNEYT ALAVELSAPP LAWITGLLPG EVLTHDAEEW R PPTSWELR HVVGEGSFTG VSGAAAAALL GMSATNFRKY TAGDSAANRQ KISFAAWHYL LDRLGVKRAS |
-Macromolecule #6: RNA (60-MER)
Macromolecule | Name: RNA (60-MER) / type: rna / ID: 6 / Number of copies: 2 |
---|---|
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 |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: DARK FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |