8SFJ: WT CRISPR-Cas12a with a 10bp R-loop

WT CRISPR-Cas12a with a 10bp R-loop. Determined by electron microscopy at 3.6 Å resolution. Released 3 Jul 2024.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Acidaminococcus sp. BV3L6, synthetic construct
Chains: 4
Atoms: 10,207
Mol. weight: 201.57 kDa
Released: 3 Jul 2024

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

Secondary structure: helices and β-sheets

8SFJ contains 49 α-helices and 42 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: 49 helices, 42 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	27-34	8
α-helix	36-66	31
α-helix	74-86	13
α-helix	89-111	23
α-helix	119-131	13
α-helix	135-137	3
α-helix	141-145	5
α-helix	153-160	8
α-helix	166-169	4
α-helix	170-180	11
α-helix	189-190	2
α-helix	191-197	7
α-helix	198-214	17
α-helix	217-229	13
α-helix	237-240	4
α-helix	243-247	5
α-helix	252-263	12
α-helix	277-286	10
α-helix	290-296	7
α-helix	306-308	3
β-strand	531-533	3	3
α-helix	549-552	4
β-strand	554-559	6	3
β-strand	562-567	6	3
α-helix	580-582	3
β-strand	589-597	9	3
α-helix	601-604	4
α-helix	613-621	9
β-strand	626-628	3	4
β-strand	632	1	5
β-strand	636-638	3	4
α-helix	640-646	7
α-helix	657-663	7
α-helix	666-686	21
β-strand	687	1	5
α-helix	699-700	2
α-helix	701-703	3
α-helix	707-714	8
α-helix	715-718	4
β-strand	719-727	9	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
β-strand	868-877	10	3
β-strand	882	1	2
α-helix	888-898	11
β-strand	904-909	6	6
β-strand	915-920	6	6
β-strand	926-931	6	6
β-strand	934	1	7
β-strand	939	1	7
α-helix	941-948	8
α-helix	965-986	22
β-strand	989-993	5	6
α-helix	995-997	3
α-helix	1009-1024	16
β-strand	1026	1	1
β-strand	1043	1	1
α-helix	1047-1049	3
β-strand	1059	1	6
β-strand	1062-1065	4	6
β-strand	1083	1	8
α-helix	1091-1099	9
β-strand	1103-1106	4	9
β-strand	1113-1118	6	9
β-strand	1126	1	8
β-strand	1135-1140	6	9
β-strand	1145-1147	3	10
β-strand	1153-1155	3	10
β-strand	1159-1161	3	11
β-strand	1164-1165	2	12
β-strand	1168-1169	2	12
β-strand	1174-1176	3	11
α-helix	1178-1186	9
α-helix	1199-1205	7
α-helix	1209-1223	15
β-strand	1226-1229	4	13
β-strand	1234-1237	4	13
β-strand	1238-1242	5	14
β-strand	1248-1250	3	14
α-helix	1251-1253	3
α-helix	1262-1283	22
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 (29-mer)	B	RNA	48	synthetic construct
DNA (5'-d(pcpapcptptpaptpcpapcptpapapapapgpaptpcpgpgpapapg)-3')	C	DNA	56	synthetic construct
DNA (5'-d(pcptptpcpcpgpaptpcptptptptpapgptpgpap*t)-3')	D	DNA	56	synthetic construct

Sequence of entity 1 (A), FASTA

>8SFJ_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

>8SFJ_2 RNA (29-MER) (chains B)
UUUUUAAUUUCUACUCUUGUAGAUGUGAUAAGUGGAAUGCCAUGUGGA

Sequence of entity 3 (C), FASTA

>8SFJ_3 DNA (5'-D(P*CP*AP*CP*TP*TP*AP*TP*CP*AP*CP*TP*AP*AP*AP*AP*GP*AP*TP*CP*GP*GP*AP*AP*G)-3') (chains C)
AGCACAGTAGCTACTCCAGTACCGTATCCACTTATCACTAAAAGATCGGAAGAGCG

Sequence of entity 4 (D), FASTA

>8SFJ_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)
CGCTCTTCCGATCTTTTAGTGATAAGTGGATACGGTACTGGAGTAGCTACTGTGCT

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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