Structure of double-stranded target DNA engaged Csy complex from Pseudomonas aeruginosa (PA-14)

2019-03-20 REL RCSB RCSB RCSB 2018-10-08 2018-10-24 2018-10-24 2019-03-20 Structure of double-stranded target DNA engaged Csy complex from Pseudomonas aeruginosa (PA-14) Chowdhury S Rollins MF Carter J Golden SM Miettinen HM Santiago-Frangos A Faith D Lawrence MC Wiedenheft B Lander GC Rollins MF Chowdhury S Carter J Golden SM Miettinen HM Santiago-Frangos A Faith D Lawrence MC Wiedenheft B Lander GC Structure Reveals a Mechanism of CRISPR-RNA-Guided Nuclease Recruitment and Anti-CRISPR Viral Mimicry Mol.Cell US 2019 doi:10.1016/j.molcel.2019.02.001 1097-2765 2168 MOCEFL EMD-9191 associated EM volume

6mpu FULLOVERLAP Double-stranded target DNA engaged Csy Complex from Pseudomonas aeruginosa (PA-14) Double-stranded target DNA engaged Csy Complex from Pseudomonas aeruginosa (PA-14) 0 1 2 3 4 5 6 7 Pseudomonas aeruginosa (strain UCBPP-PA14) Escherichia coli BL21(DE3) 0.36 CRISPR-associated protein Csy2 Pseudomonas aeruginosa (strain UCBPP-PA14) UCBPP-PA14 0.036244074 1 Escherichia coli BL21(DE3) LEVO MSVTDPEALLLLPRLSIQNANAISSPLTWGFPSPGAFTGFVHALQRRVGISLDIELDGVGIVCHRFEAQISQPAGKRTKV FNLTRNPLNRDGSTAAIVEEGRAHLEVSLLLGVHGDGLDDHPAQEIARQVQEQAGAMRLAGGSILPWCNERFPAPNAELL MLGGSDEQRRKNQRRLTRRLLPGFALVSREALLQQHLETLRTTLPEATTLDALLDLCRINFEPPATSSEEEASPPDAAWQ VRDKPGWLVPIPAGYNALSPLYLPGEVRNARDRETPLRFVENLFGLGEWLSPHRVAALSDLLWYHHAEPDKGLYRWSTPR FVEHAIA CRISPR-associated protein Csy3 Pseudomonas aeruginosa (strain UCBPP-PA14) UCBPP-PA14 0.037579273 6 Escherichia coli BL21(DE3) LEVO MSKPILSTASVLAFERKLDPSDALMSAGAWAQRDASQEWPAVTVREKSVRGTISNRLKTKDRDPAKLDASIQSPNLQTVD VANLPSDADTLKVRFTLRVLGGAGTPSACNDAAYRDKLLQTVATYVNDQGFAELARRYAHNLANARFLWRNRVGAEAVEV RINHIRQGEVARAWRFDALAIGLRDFKADAELDALAELIASGLSGSGHVLLEVVAFARIGDGQEVFPSQELILDKGDKKG QKSKTLYSVRDAAAIHSQKIGNALRTIDTWYPDEDGLGPIAVEPYGSVTSQGKAYRQPKQKLDFYTLLDNWVLRDEAPAV EQQHYVIANLIRGGVFGEAEEK CRISPR-associated endonuclease Cas6/Csy4 Pseudomonas aeruginosa (strain UCBPP-PA14) UCBPP-PA14 0.021675781 1 Escherichia coli BL21(DE3) LEVO FTMDHYLDIRLRPDPEFPPAQLMSVLFGKLHQALVAQGGDRIGVSFPDLDESRSRLGERLRIHASADDLRALLARPWLEG LRDHLQFGEPAVVPHPTPYRQVSRVQAKSNPERLRRRLMRRHDLSEEEARKRIPDTVARALDLPFVTLRSQSTGQHFRLF IRHGPLQVTAEEGGFTCYGLSKGGFVPWF 3.1.-.- CRISPR RNA (60-MER) Pseudomonas aeruginosa UCBPP-PA14 0.019265404 1 CUAAGAAAUUCACGGCGGGCUUGAUGUCCGCGUCUACCUGGUUCACUGCCGUGUAGGCAG CRISPR target DNA (44-MER) Pseudomonas aeruginosa UCBPP-PA14 0.013584703 1 (DC)(DA)(DG)(DG)(DT)(DA)(DG)(DA)(DC)(DG)(DC)(DG)(DG)(DA)(DC)(DA)(DT)(DC)(DA)(DA) (DG)(DC)(DC)(DC)(DG)(DC)(DC)(DG)(DT)(DG)(DA)(DA)(DG)(DG)(DT)(DG)(DC)(DA)(DG)(DC) (DT)(DT)(DC)(DT) DNA Non-complementary R-loop DNA strand Pseudomonas aeruginosa UCBPP-PA14 0.010476714 1 (DA)(DG)(DA)(DA)(DG)(DC)(DT)(DG)(DC)(DA)(DC)(DC)(DT)(DT)(DC)(DA)(DC)(DG)(DG)(DC) (DG)(DG)(DG)(DC)(DT)(DT)(DG)(DA)(DT)(DG)(DT)(DC)(DC)(DG) DNA CRISPR-associated protein Csy1 Pseudomonas aeruginosa (strain UCBPP-PA14) UCBPP-PA14 0.049194168 1 Escherichia coli BL21(DE3) LEVO MTSPLPTPTWQELRQFIESFIQERLQGKLDKLQPDEDDKRQTLLATHRREAWLADAARRVGQLQLVTHTLKPIHPDARGS NLHSLPQAPGQPGLAGSHELGDRLVSDVVGNAAALDVFKFLSLQYQGKNLLNWLTEDSAEALQALSDNAEQAREWRQAFI GITTVKGAPASHSLAKQLYFPLPGSGYHLLAPLFPTSLVHHVHALLREARFGDAAKAAREARSRQESWPHGFSEYPNLAI QKFGGTKPQNISQLNNERRGENWLLPSLPPNWQRQNVNAPMRHSSVFEHDFGRTPEVSRLTRTLQRFLAKTVHNNLAIRQ RRAQLVAQICDEALQYAARLRELEPGWSATPGCQLHDAEQLWLDPLRAQTDETFLQRRLRGDWPAEVGNRFANWLNRAVS SDSQILGSPEAAQWSQELSKELTMFKEILEDERD singleParticle particle 2 7.5 20.0 C8H18N2O4S HEPES 100.0 KCl potassium chloride 1.0 C9H15O6P TCEP 2.0 C3H8O3 glycerol 0.05 C47H88O22 lauryl maltose neopentyl glycol Quantifoil, UltrAuFoil, R1.2/1.3 PLASMA CLEANING OTHER ETHANE HOMEMADE PLUNGER

Freezing was carried out in a cold room at 4 degrees C and relative humidity of 98%. 5 uL sample was applied to plasma cleaned grid and manually blotted with Whatman 1 filter paper for 5-7 sec before plunge freezing..

FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 70.0 2.7 0.6 1.5 36000. FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 77.0 79.0

Objective astigmatism was corrected at 36000x magnification using Thon rings visualized with a K2 camera.

GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 7676 7420 2.5 1-56 4 3208 14.0 58.0

Data were acquired using Leginon and collected on K2 summit operating in super-resolution mode.

Super-resolution movie frames were Fourier-binned 2 x 2 times to a pixel size of 1.15 Angstrom/pixel prior to dose-weighted frame alignment using MotionCorr2.

1543677

Particles were initially extracted binned by 2 with a box size of 144 pixels (2.3 Angstrom/pixel). The final processing was carried out with an unbinned particle stack with a box size of 288 pixels (1.15 Angstrom/pixel).

CTFFIND 4 EMD-8624

This map was low pass-filtered to 60 Angstrom and used as initial model for 3D reconstruction and data processing.

C1 FOURIER SPACE 3.4 FSC 0.143 CUT-OFF

The final map was reconstructed using several focused maps from different subregions of the complex. These were initially aligned to each other and then stitched using the vop maximum function in UCSF Chimera. The resolution of the final composite map is 3.2 Angstrom.

291227 MAXIMUM LIKELIHOOD RELION 2.0 MAXIMUM LIKELIHOOD RELION 2.1 emd_9191.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 184.0 184.0 184.0 90.0 90.0 90.0 X Y Z -0.121736825 0.27672002 0.0024644134 0.016295806 1.15 1.15 1.15 0.0595 AUTHOR ::::EMDATABANK.org::::EMD-9191:::: Composite sharpened map of the complex generated from multiple focused maps of different sub-regions of the complex. A B-factor of -35 was used for sharpening the map. 5UZ9 AB INITIO MODEL

The atomic models for Cas5f, Cas8f, Cas6f, and Cas7f from the Csy Acr complex (PDB ID 5UZ9) were used as initial template models for model building. These were individually rigid body-fitted into the reconstructed maps using the fit map function in UCSF Chimera, and residue registers and backbone geometries were fixed in Coot. Models for the crRNA and DNA strands were also manually built into the map using Coot.

REAL emd_9191_msk_1.map emd_9191_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 184.0 184.0 184.0 90.0 90.0 90.0 X Y Z -0.008412552 0.06332772 0.0007500944 0.005487023 1.15 1.15 1.15 AUTHOR ::::EMDATABANK.org::::EMD-9191:::: Composite unsharpened map of the complex generated from multiple focused maps of different sub-regions of the complex emd_9191_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 184.0 184.0 184.0 90.0 90.0 90.0 X Y Z -0.023284994 0.06178115 -0.0008198236 0.0031323656 1.15 1.15 1.15 AUTHOR ::::EMDATABANK.org::::EMD-9191:::: Focused map of "Region-3" of the Csy-DNA complex, comprising the tail (Cas8f N-terminal half - Cas5f - double-stranded target DNA) - Cas7.6 subunit emd_9191_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 184.0 184.0 184.0 90.0 90.0 90.0 X Y Z -0.024919301 0.06055068 -0.000666881 0.0035465488 1.15 1.15 1.15 AUTHOR ::::EMDATABANK.org::::EMD-9191:::: Focused map of "Region-1" of the Csy-DNA complex, comprising the head (Cas6f-crRNA stem loop) - Cas8f C-terminal helix bundle - Cas7.1f and Cas7.2f subunits emd_9191_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 184.0 184.0 184.0 90.0 90.0 90.0 X Y Z -0.019688675 0.06332772 -0.0004685645 0.0044685504 1.15 1.15 1.15 AUTHOR ::::EMDATABANK.org::::EMD-9191:::: Focused map of "Region-2" of the Csy-DNA complex, comprising all six Cas7f subunits - crRNA - complimentary target DNA strand emd_9191_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 184.0 184.0 184.0 90.0 90.0 90.0 X Y Z -0.3029115 0.51139647 0.00009941576 0.026230076 1.15 1.15 1.15 AUTHOR ::::EMDATABANK.org::::EMD-9191:::: Sharpened non-focused map of the full complex emd_9191_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 184.0 184.0 184.0 90.0 90.0 90.0 X Y Z -0.018827714 0.06145127 0.000047248952 0.0051037883 1.15 1.15 1.15 AUTHOR ::::EMDATABANK.org::::EMD-9191:::: Unsharpened non-focused map of the full complex emd_9191_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 184.0 184.0 184.0 90.0 90.0 90.0 X Y Z -0.008589858 0.06654455 0.0011923522 0.005479196 1.15 1.15 1.15 AUTHOR ::::EMDATABANK.org::::EMD-9191:::: Unfiltered composite half map #2 emd_9191_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 184.0 184.0 184.0 90.0 90.0 90.0 X Y Z -0.00909429 0.06848169 0.0012445793 0.005502481 1.15 1.15 1.15 AUTHOR ::::EMDATABANK.org::::EMD-9191:::: Unfiltered composite half map #1