Cryo EM structure of anti-CRISPRs, AcrF1 and AcrF2, bound to type I-F crRNA-guided CRISPR surveillance complex

2024-03-13 REL RCSB RCSB RCSB 2017-02-25 2017-04-26 2017-04-26 2024-03-13 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) P20GM103500, P30GM110732-03, R01GM110270, R01GM108888, P20GM103474, F32GM108436, DP2EB020402, DP5OD021344 United States National Science Foundation (NSF, United States) EPS-110134 United States Canadian Institutes of Health Research (CIHR) MOP-130482, MOP-136845 Canada Cryo EM structure of anti-CRISPRs, AcrF1 and AcrF2, bound to type I-F crRNA-guided CRISPR surveillance complex Chowdhury S Carter J CRISPR RNA-recognition-motif (RRM), pseudo-helical, Type 1-F CRISPR, IMMUNE SYSTEM-RNA complex Chowdhury S Carter J Rollins MF Golden SM Jackson RN Hoffmann C Nosaka L Bondy-Denomy J Maxwell KL Davidson AR Fischer ER Lander GC Wiedenheft B Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex. Cell 169 47 57.e11 2017 28340349 doi:10.1016/j.cell.2017.03.012 1097-4172 5uz9 FULLOVERLAP Anti-CRISPRs AcrF1 and AcrF2 bound P. aeruginosa crRNA-guided CRISPR surveillance(Csy)complex. Anti-CRISPRs AcrF1 and AcrF2 bound P. aeruginosa crRNA-guided CRISPR surveillance(Csy)complex. 0 1 2 3 4 5 6 7

Cas5F, Cas6F, Cas7F, Cas8F and CRISPR RNA (crRNA) forms the Csy surveillance complex. Cas5F, Cas8F and 5'crRNA handle forms the "tail" of the complex, and 3' crRNA stem-loop along with Cas6F forms the "head". Six copies Cas7F along with crRNA spacer forms the "core" of the complex.

Pseudomonas aeruginosa UCBPP-PA14 0.45 CRISPR-associated protein Csy1 Pseudomonas aeruginosa (strain UCBPP-PA14) UCBPP-PA14 0.049194167999999996 1 Escherichia coli BL21(DE3) LEVO MTSPLPTPTWQELRQFIESFIQERLQGKLDKLQPDEDDKRQTLLATHRREAWLADAARRVGQLQLVTHTLKPIHPDARGS NLHSLPQAPGQPGLAGSHELGDRLVSDVVGNAAALDVFKFLSLQYQGKNLLNWLTEDSAEALQALSDNAEQAREWRQAFI GITTVKGAPASHSLAKQLYFPLPGSGYHLLAPLFPTSLVHHVHALLREARFGDAAKAAREARSRQESWPHGFSEYPNLAI QKFGGTKPQNISQLNNERRGENWLLPSLPPNWQRQNVNAPMRHSSVFEHDFGRTPEVSRLTRTLQRFLAKTVHNNLAIRQ RRAQLVAQICDEALQYAARLRELEPGWSATPGCQLHDAEQLWLDPLRAQTDETFLQRRLRGDWPAEVGNRFANWLNRAVS SDSQILGSPEAAQWSQELSKELTMFKEILEDERD Q02ML9 CRISPR-associated protein Csy2 Pseudomonas aeruginosa (strain UCBPP-PA14) UCBPP-PA14 0.036244074 1 Escherichia coli BL21(DE3) LEVO MSVTDPEALLLLPRLSIQNANAISSPLTWGFPSPGAFTGFVHALQRRVGISLDIELDGVGIVCHRFEAQISQPAGKRTKV FNLTRNPLNRDGSTAAIVEEGRAHLEVSLLLGVHGDGLDDHPAQEIARQVQEQAGAMRLAGGSILPWCNERFPAPNAELL MLGGSDEQRRKNQRRLTRRLLPGFALVSREALLQQHLETLRTTLPEATTLDALLDLCRINFEPPATSSEEEASPPDAAWQ VRDKPGWLVPIPAGYNALSPLYLPGEVRNARDRETPLRFVENLFGLGEWLSPHRVAALSDLLWYHHAEPDKGLYRWSTPR FVEHAIA Q02MM0 CRISPR-associated protein Csy3 Pseudomonas aeruginosa (strain UCBPP-PA14) UCBPP-PA14 0.037448078 6 Escherichia coli BL21(DE3) LEVO SKPILSTASVLAFERKLDPSDALMSAGAWAQRDASQEWPAVTVREKSVRGTISNRLKTKDRDPAKLDASIQSPNLQTVDV ANLPSDADTLKVRFTLRVLGGAGTPSACNDAAYRDKLLQTVATYVNDQGFAELARRYAHNLANARFLWRNRVGAEAVEVR INHIRQGEVARAWRFDALAIGLRDFKADAELDALAELIASGLSGSGHVLLEVVAFARIGDGQEVFPSQELILDKGDKKGQ KSKTLYSVRDAAAIHSQKIGNALRTIDTWYPDEDGLGPIAVEPYGSVTSQGKAYRQPKQKLDFYTLLDNWVLRDEAPAVE QQHYVIANLIRGGVFGEAEEK Q02MM1 Anti-CRISPR protein Acr30-35 Pseudomonas phage JBD30 0.008693734 2 Escherichia coli BL21(DE3) LEVO KFIKYLSTAHLNYMNIAVYENGSKIKARVENVVNGKSVGARDFDSTEQLESWFYGLPGSGLGRIENAMNEISRRENP L7P7M1 Anti-CRISPR protein 30 Pseudomonas phage D3112 0.010760480999999999 1 Escherichia coli BL21(DE3) LEVO MHHHHHHIAQQHKDTVAACEAAEAIAIAKDQVWDGEGYTKYTFDDNSVLIQSGTTQYAMDADDADSIKGYADWLDDEARS AEASEIERLLESVEEE Q6TM72 CRISPR-associated endonuclease Cas6/Csy4 Pseudomonas aeruginosa (strain UCBPP-PA14) UCBPP-PA14 0.021691848 1 Escherichia coli BL21(DE3) LEVO FTMDHYLDIRLRPDPEFPPAQLMCVLFGKLHQALVAQGGDRIGVSFPDLDESRSRLGERLRIHASADDLRALLARPWLEG LRDHLQFGEPAVVPHPTPYRQVSRVQAKSNPERLRRRLMRRHDLSEEEARKRIPDTVARALDLPFVTLRSQSTGQHFRLF IRHGPLQVTAEEGGFTCYGLSKGGFVPWF Q02MM2 3.1.-.- CRISPR RNA (60-MER) Pseudomonas aeruginosa UCBPP-PA14 0.019249403999999998 1 CUAAGAAAUUCACGGCGGGCUUGAUGUCCGCGUCUACCUGGUUCACUGCCGUAUAGGCAG CP000438.1 singleParticle particle 0.1 7.5 20.0 C4H11NO3 Tris 100.0 KCl Potassium Chloride 1.0 C9H15O6P TCEP

Buffer was filtered before use.

C-flat-2/2 COPPER 400 CARBON HOLEY PLASMA CLEANING 5 OTHER

Holey grid was coated with an amorphous carbon film.

ETHANE 98 277 HOMEMADE PLUNGER

Sample was applied to poly-L-lysine hydrobromide pre-treated amorphous carbon film coated over a holey grid. Excess sample was blotted with Whatman-1 filter paper and plunge frozen. Manual plunge freezing was performed in a cold room..

Sample was free from any aggregation and monodisperse.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.2 2.5 29000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 77.0 79.0

Objective astigmatism was corrected at nominal magnification of 29000X, using Thon rings visualized with a K2 camera.

GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 1-30 2 2261 6.0 46.0

Images were collected in movie mode using Leginon automated data acquisition software. Movie frames were aligned using MotionCorr program.

Raw movie frames were aligned using MotionCorr.

199348

Template based particle picking was done using FindEM program implemented in Appion processing package.

A negative stain reconstruction was used as initial model.

1 C1 FOURIER SPACE 3.4 FSC 0.143 CUT-OFF RELION 1.4

Per-frame dose weighting was performed using the RELION particle polishing method. A B-factor of -71 square angstrom was applied to sharpen the final map. Signal subtracted focused classification and refinement was performed for the "tail" region of the complex. This lead to a 4 angstrom (Gold standard FSC 0.143) map.

51212 NOT APPLICABLE RELION 1.4 PROJECTION MATCHING RELION 1.4 RELION 1.4 emd_8624.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 210 210 210 0 0 0 210 210 210 216.29999 216.29999 216.29999 90.0 90.0 90.0 X Y Z -0.10289869 0.17144284 0.0007336988 0.006945551 1.03 1.03 1.03 0.0274 AUTHOR ::::EMDATABANK.org::::EMD-8624:::: Cryo EM map of the Csy-Acr complex. AB INITIO MODEL

Top scoring five models out of two hundred models generated using Rosetta were refined using Phenix and deposited as an ensemble atomic model for the final EM map.

REAL RIGID BODY FIT

The docked Cas6F structure in the "head" region of the complex was reduced to C-alpha backbone.

REAL RIGID BODY FIT

Initially two copies were fitted using Chimera and then backbones and side chains were fixed using Coot, followed by real space refinement in Phenix.

REAL emd_8624_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 210 210 210 0 0 0 210 210 210 216.29999 216.29999 216.29999 90.0 90.0 90.0 X Y Z -0.063441195 0.12319797 0.00019210875 0.0030031581 1.03 1.03 1.03 AUTHOR ::::EMDATABANK.org::::EMD-8624:::: Focused map of the "tail" region of Csy-Acr complex, comprising of Cas5, Cas8 and Acr2 subunits. emd_8624_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 210 210 210 0 0 0 210 210 210 216.29999 216.29999 216.29999 90.0 90.0 90.0 X Y Z -0.008322517 0.022550693 0.00007880698 0.001777823 1.03 1.03 1.03 AUTHOR ::::EMDATABANK.org::::EMD-8624:::: Unsharpened Cryo EM map of the Csy-Acr complex. emd_8624_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 210 210 210 0 0 0 210 210 210 216.29999 216.29999 216.29999 90.0 90.0 90.0 X Y Z -0.016158575 0.03853382 0.00035099825 0.0020112519 1.03 1.03 1.03 AUTHOR ::::EMDATABANK.org::::EMD-8624:::: Half-map 2 of the Csy-Acr complex. emd_8624_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 210 210 210 0 0 0 210 210 210 216.29999 216.29999 216.29999 90.0 90.0 90.0 X Y Z -0.01599704 0.03475953 0.00035211217 0.002020524 1.03 1.03 1.03 AUTHOR ::::EMDATABANK.org::::EMD-8624:::: Half-map 1 of the Csy-Acr complex.