9CJI: CRISPR-associated endonuclease Cas12a

Cas12a:gRNA:DNA (Acidaminococcus sp.) with 0 RNA:DNA base pairs, structure 2. Determined by electron microscopy at 3.4 Å resolution. Released 8 Jan 2025.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: synthetic construct, Acidaminococcus sp. BV3L6
Chains: 4
Atoms: 11,477
Mol. weight: 184.22 kDa
Released: 8 Jan 2025

Explore 9CJI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CJI contains 63 α-helices and 54 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: 63 helices, 54 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	36-67	32
α-helix	74-85	12
α-helix	89-111	23
α-helix	119-130	12
α-helix	135-137	3
α-helix	141-145	5
α-helix	153-160	8
α-helix	170-180	11
α-helix	189-191	3
α-helix	192-197	6
α-helix	198-214	17
α-helix	217-229	13
α-helix	243-248	6
α-helix	252-263	12
α-helix	326-343	18
α-helix	345-355	11
α-helix	361-363	3
β-strand	365-366	2	4
α-helix	368-378	11
α-helix	383-394	12
α-helix	403-414	12
α-helix	417	1
β-strand	418-419	2	4
α-helix	420-427	8
α-helix	429-450	22
α-helix	453-454	2
α-helix	461-481	21
β-strand	484	1	4
α-helix	494-506	13
α-helix	509-521	13
β-strand	531-532	2	3
β-strand	545	1	5
α-helix	549-552	4
β-strand	555-559	5	3
β-strand	562-567	6	3
β-strand	571	1	6
β-strand	574	1	6
β-strand	582	1	5
β-strand	589-596	8	5
α-helix	601-605	5
α-helix	606-610	5
α-helix	613-621	9
β-strand	626-628	3	7
β-strand	632	1	8
α-helix	635	1
β-strand	636-638	3	7
α-helix	640-646	7
α-helix	657-663	7
α-helix	666-686	21
β-strand	687	1	8
α-helix	695-697	3
α-helix	699-700	2
α-helix	707-718	12
β-strand	720-727	8	5
α-helix	728-737	10
β-strand	741-746	6	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	799-800	2	9
β-strand	805-809	5	10
β-strand	810	1	11
β-strand	811	1	10
β-strand	817	1	11
α-helix	818-819	2
α-helix	820-830	11
α-helix	837-839	3
α-helix	840-845	6
α-helix	846-848	3
β-strand	849-853	5	10
β-strand	858-859	2	9
α-helix	862-864	3
β-strand	868-877	10	3
β-strand	882	1	2
α-helix	888-898	11
β-strand	904-908	5	12
β-strand	916-920	5	12
β-strand	926-931	6	12
β-strand	934	1	13
β-strand	939	1	13
α-helix	940-945	6
α-helix	946-955	10
α-helix	959-986	28
α-helix	988	1
β-strand	989-994	6	12
α-helix	1011-1024	14
β-strand	1026	1	1
β-strand	1043	1	1
α-helix	1047-1049	3
β-strand	1058-1059	2	12
β-strand	1062-1066	5	12
β-strand	1083	1	14
α-helix	1091-1100	10
β-strand	1103-1107	5	15
β-strand	1112-1118	7	15
β-strand	1126	1	14
β-strand	1135-1140	6	15
β-strand	1145-1147	3	16
β-strand	1153-1155	3	16
β-strand	1159-1161	3	17
β-strand	1174-1176	3	17
α-helix	1178-1188	11
α-helix	1200-1206	7
α-helix	1209-1223	15
β-strand	1226-1229	4	18
β-strand	1234-1237	4	18
β-strand	1238-1242	5	19
β-strand	1248-1250	3	19
α-helix	1251-1253	3
α-helix	1262-1283	22
α-helix	1295-1306	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Non-target DNA strand	C	DNA	31	synthetic construct
guide RNA (25-MER)	B	RNA	42	synthetic construct
Target DNA strand	D	DNA	31	synthetic construct
CRISPR-associated endonuclease Cas12a	A	protein	1310	Acidaminococcus sp. BV3L6	U2UMQ6 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>9CJI_1 Non-target DNA strand (chains C)
GTAGTGXTTTGTCGTCTCATCTGTATGCGTC

Sequence of entity 2 (B), FASTA

>9CJI_2 guide RNA (25-MER) (chains B)
UUUAAUUUCUACUCUUGUAGAUAGCAGAGUAGACAUACGCAG

Sequence of entity 3 (D), FASTA

>9CJI_3 Target DNA strand (chains D)
GACGCATACAGATGAGACGACAAAGCACTAC

Sequence of entity 4 (A), FASTA

>9CJI_4 CRISPR-associated endonuclease Cas12a (chains A)
SNAMTQFEGFTNLYQVSKTLRFELIPQGKTLKHIQEQGFIEEDKARNDHYKELKPIIDRI
YKTYADQCLQLVQLDWENLSAAIDSYRKEKTEETRNALIEEQATYRNAIHDYFIGRTDNL
TDAINKRHAEIYKGLFKAELFNGKVLKQLGTVTTTEHENALLRSFDKFTTYFSGFYENRK
NVFSAEDISTAIPHRIVQDNFPKFKENCHIFTRLITAVPSLREHFENVKKAIGIFVSTSI
EEVFSFPFYNQLLTQTQIDLYNQLLGGISREAGTEKIKGLNEVLNLAIQKNDETAHIIAS
LPHRFIPLFKQILSDRNTLSFILEEFKSDEEVIQSFCKYKTLLRNENVLETAEALFNELN
SIDLTHIFISHKKLETISSALCDHWDTLRNALYERRISELTGKITKSAKEKVQRSLKHED
INLQEIISAAGKELSEAFKQKTSEILSHAHAALDQPLPTTLKKQEEKEILKSQLDSLLGL
YHLLDWFAVDESNEVDPEFSARLTGIKLEMEPSLSFYNKARNYATKKPYSVEKFKLNFQM
PTLASGWDVNKEKCNGAILFVKNGLYYLGIMPKQKGRYKALSFEPTEKTSEGFDKMYYDY
FPDAAKMIPKCSTQLKAVTAHFQTHTTPILLSNNFIEPLEITKEIYDLNNPEKEPKKFQT
AYAKKTGDQKGYREALCKWIDFTRDFLSKYTKTTSIDLSSLRPSSQYKDLGEYYAELNPL
LYHISFQRIAEKEIMDAVETGKLYLFQIYNKDFAKGHHGKPNLHTLYWTGLFSPENLAKT
SIKLNGQAELFYRPKSRMKRMAHRLGEKMLNKKLKDQKTPIPDTLYQELYDYVNHRLSHD
LSDEARALLPNVITKEVSHEIIKDRRFTSDKFFFHVPITLNYQAANSPSKFNQRVNAYLK
EHPETPIIGIDRGERNLIYITVIDSTGKILEQRSLNTIQQFDYQKKLDNREKERVAARQA
WSVVGTIKDLKQGYLSQVIHEIVDLMIHYQAVVVLENLNFGFKSKRTGIAEKAVYQQFEK
MLIDKLNCLVLKDYPAEKVGGVLNPYQLTDQFTSFAKMGTQSGFLFYVPAPYTSKIDPLT
GFVDPFVWKTIKNHESRKHFLEGFDFLHYDVKTGDFILHFKMNRNLSFQRGLPGFMPAWD
IVFEKNETQFDAKGTPFIAGKRIVPVIENHRFTGRYRDLYPANELIALLEEKGIVFRDGS
NILPKLLENDDSHAIDTMVALIRSVLQMRNSNAATGEDYINSPVRDLNGVCFDSRFQNPE
WPMDADANGAYHIALKGQLLLNHLKESKDLKLQNGISNQDWLAYIQELRN

Primary citation

CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation. Soczek, K.M., Cofsky, J.C., Tuck, O.T. et al. Nucleic Acids Res (2025) 53. DOI 10.1093/nar/gkae1192 · 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
8SFI 3.5 Å, WT CRISPR-Cas12a with a 8bp R-loop

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