8SFQ: CRISPR-associated endonuclease Cas12a

WT CRISPR-Cas12a post nontarget strand-cleavage with the the RuvC active site exposed. Determined by electron microscopy at 3.5 Å resolution. Released 3 Jul 2024.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Acidaminococcus sp. BV3L6, synthetic construct
Chains: 4
Atoms: 12,045
Mol. weight: 201.57 kDa
Released: 3 Jul 2024

Explore 8SFQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SFQ contains 66 α-helices and 47 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 66 helices, 47 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	8	1	1
β-strand	11	1	2
β-strand	13-23	11	3
α-helix	27-32	6
α-helix	36-66	31
α-helix	74-85	12
α-helix	89-111	23
α-helix	119-129	11
α-helix	136-139	4
α-helix	143-146	4
α-helix	153-159	7
α-helix	160-162	3
α-helix	166-169	4
α-helix	170-177	8
α-helix	189-191	3
α-helix	192-197	6
α-helix	198-214	17
α-helix	218-229	12
α-helix	237-240	4
α-helix	243-247	5
α-helix	252-263	12
α-helix	272-275	4
α-helix	277-286	10
α-helix	290-297	8
α-helix	304-308	5
α-helix	326-343	18
α-helix	345-355	11
α-helix	356-358	3
α-helix	361-363	3
β-strand	365-366	2	4
α-helix	368-370	3
α-helix	371-378	8
α-helix	384-395	12
α-helix	404-415	12
β-strand	418-419	2	4
α-helix	420-427	8
α-helix	430-451	22
α-helix	461-481	21
β-strand	484	1	4
α-helix	494-507	14
α-helix	509-521	13
α-helix	524-526	3
β-strand	531-533	3	3
α-helix	549-552	4
β-strand	554-559	6	3
β-strand	562-567	6	3
β-strand	571	1	5
β-strand	574	1	5
β-strand	591-597	7	3
α-helix	601-609	9
α-helix	613-621	9
β-strand	626-628	3	6
β-strand	632	1	7
β-strand	636-638	3	6
α-helix	640-646	7
α-helix	657-663	7
α-helix	666-686	21
β-strand	687	1	7
α-helix	698-700	3
α-helix	701-703	3
α-helix	707-714	8
α-helix	715-718	4
β-strand	719-725	7	3
α-helix	728-737	10
β-strand	741-746	6	3
α-helix	757-759	3
α-helix	760-768	9
α-helix	771-775	5
β-strand	779-781	3	3
β-strand	786-790	5	3
α-helix	862-864	3
β-strand	868-877	10	3
β-strand	882	1	2
α-helix	888-898	11
β-strand	904-909	6	8
β-strand	915-920	6	8
β-strand	926-931	6	8
β-strand	934	1	9
β-strand	939	1	9
α-helix	940-956	17
α-helix	965-986	22
β-strand	989-994	6	8
α-helix	997-1006	10
α-helix	1015-1024	10
β-strand	1026	1	1
β-strand	1043	1	1
β-strand	1058-1059	2	8
β-strand	1062-1066	5	8
β-strand	1083	1	10
α-helix	1085-1087	3
α-helix	1091-1099	9
β-strand	1101-1107	7	11
β-strand	1112-1118	7	11
β-strand	1126	1	10
β-strand	1135-1140	6	11
β-strand	1145-1147	3	12
β-strand	1153-1155	3	12
β-strand	1159-1162	4	13
β-strand	1173-1176	4	13
α-helix	1178-1189	12
β-strand	1198	1	11
α-helix	1200-1204	5
α-helix	1209-1222	14
β-strand	1226-1229	4	14
β-strand	1234-1237	4	14
β-strand	1238	1	15
β-strand	1241	1	11
α-helix	1242-1243	2
β-strand	1250	1	15
α-helix	1251-1253	3
α-helix	1262-1282	21
α-helix	1295-1306	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cas12a	A	protein	1311	Acidaminococcus sp. BV3L6	U2UMQ6 (AlphaFold model)
RNA (39-mer)	B	RNA	48	synthetic construct
DNA (34-mer)	C	DNA	56	synthetic construct
DNA (5'-d(pcptptpcpcpgpaptpcptptptptpapgptpgpap*t)-3')	D	DNA	56	synthetic construct

Sequence of entity 1 (A), FASTA

>8SFQ_1 CRISPR-associated endonuclease Cas12a (chains A)
GAASMTQFEGFTNLYQVSKTLRFELIPQGKTLKHIQEQGFIEEDKARNDHYKELKPIIDR
IYKTYADQCLQLVQLDWENLSAAIDSYRKEKTEETRNALIEEQATYRNAIHDYFIGRTDN
LTDAINKRHAEIYKGLFKAELFNGKVLKQLGTVTTTEHENALLRSFDKFTTYFSGFYENR
KNVFSAEDISTAIPHRIVQDNFPKFKENCHIFTRLITAVPSLREHFENVKKAIGIFVSTS
IEEVFSFPFYNQLLTQTQIDLYNQLLGGISREAGTEKIKGLNEVLNLAIQKNDETAHIIA
SLPHRFIPLFKQILSDRNTLSFILEEFKSDEEVIQSFCKYKTLLRNENVLETAEALFNEL
NSIDLTHIFISHKKLETISSALCDHWDTLRNALYERRISELTGKITKSAKEKVQRSLKHE
DINLQEIISAAGKELSEAFKQKTSEILSHAHAALDQPLPTTLKKQEEKEILKSQLDSLLG
LYHLLDWFAVDESNEVDPEFSARLTGIKLEMEPSLSFYNKARNYATKKPYSVEKFKLNFQ
MPTLASGWDVNKEKNNGAILFVKNGLYYLGIMPKQKGRYKALSFEPTEKTSEGFDKMYYD
YFPDAAKMIPKCSTQLKAVTAHFQTHTTPILLSNNFIEPLEITKEIYDLNNPEKEPKKFQ
TAYAKKTGDQKGYREALCKWIDFTRDFLSKYTKTTSIDLSSLRPSSQYKDLGEYYAELNP
LLYHISFQRIAEKEIMDAVETGKLYLFQIYNKDFAKGHHGKPNLHTLYWTGLFSPENLAK
TSIKLNGQAELFYRPKSRMKRMAHRLGEKMLNKKLKDQKTPIPDTLYQELYDYVNHRLSH
DLSDEARALLPNVITKEVSHEIIKDRRFTSDKFFFHVPITLNYQAANSPSKFNQRVNAYL
KEHPETPIIGIDRGERNLIYITVIDSTGKILEQRSLNTIQQFDYQKKLDNREKERVAARQ
AWSVVGTIKDLKQGYLSQVIHEIVDLMIHYQAVVVLENLNFGFKSKRTGIAEKAVYQQFE
KMLIDKLNCLVLKDYPAEKVGGVLNPYQLTDQFTSFAKMGTQSGFLFYVPAPYTSKIDPL
TGFVDPFVWKTIKNHESRKHFLEGFDFLHYDVKTGDFILHFKMNRNLSFQRGLPGFMPAW
DIVFEKNETQFDAKGTPFIAGKRIVPVIENHRFTGRYRDLYPANELIALLEEKGIVFRDG
SNILPKLLENDDSHAIDTMVALIRSVLQMRNSNAATGEDYINSPVRDLNGVCFDSRFQNP
EWPMDADANGAYHIALKGQLLLNHLKESKDLKLQNGISNQDWLAYIQELRN

Sequence of entity 2 (B), FASTA

>8SFQ_2 RNA (39-MER) (chains B)
UUUUUAAUUUCUACUCUUGUAGAUGUGAUAAGUGGAAUGCCAUGUGGA

Sequence of entity 3 (C), FASTA

>8SFQ_3 DNA (34-MER) (chains C)
AGCACAGTAGCTACTCCACATGGCATTCCACTTATCACTAAAAGATCGGAAGAGCG

Sequence of entity 4 (D), FASTA

>8SFQ_4 DNA (5'-D(P*CP*TP*TP*CP*CP*GP*AP*TP*CP*TP*TP*TP*TP*AP*GP*TP*GP*AP*T)-3') (chains D)
CGCTCTTCCGATCTTTTAGTGATAAGTGGAATGCCATGTGGAGTAGCTACTGTGCT

Primary citation

Cas12a domain flexibility guides R-loop formation and forces RuvC resetting. Strohkendl, I., Saha, A., Moy, C. et al. Mol Cell (2024) 84:2717-2731.e6. DOI 10.1016/j.molcel.2024.06.007 · PubMed

Other PDB entries of the same protein (UniProt U2UMQ6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5XH6 2.0 Å, Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RVR variant in complex with…
5XH7 2.0 Å, Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RR variant in complex with crRNA…
9MK3 2.7 Å, Engineered AsCas12a (M537R, F870L)
5B43 2.8 Å, Crystal structure of Acidaminococcus sp. Cpf1 in complex with crRNA and target DNA
22FN 3.17 Å, Cryo-EM structure of AsCas12a in complex with crDNA and RNA target
11VQ 3.18 Å, DNA-guided AsCas12a
5KK5 3.29 Å, AsCpf1(E993A)-crRNA-DNA ternary complex
8SFL 3.3 Å, WT CRISPR-Cas12a with a 15bp R-loop
8SFN 3.3 Å, WT CRISPR-Cas12a with a 16bp R-loop and nontarget strand in the RuvC active site.
8SFO 3.3 Å, WT CRISPR-Cas12a with a 20bp R-loop and nontarget strand in the RuvC active site.
8SFH 3.4 Å, WT CRISPR-Cas12a with a 5bp R-loop
9CJI 3.4 Å, Cas12a:gRNA:DNA (Acidaminococcus sp.) with 0 RNA:DNA base pairs, structure 2

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