9MK3: Engineered AsCas12a

Engineered AsCas12a (M537R, F870L). Determined by X-ray diffraction at 2.7 Å resolution. Released 24 Dec 2025.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Acidaminococcus
Chains: 8
Atoms: 24,407
Mol. weight: 358.62 kDa
Released: 24 Dec 2025

Explore 9MK3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MK3 contains 157 α-helices and 101 β-strands across 2 chains. 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: 81 helices, 49 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	13-23	11	1
α-helix	27-34	8
α-helix	36-66	31
α-helix	74-85	12
α-helix	89-111	23
α-helix	119-129	11
α-helix	135-138	4
α-helix	141-144	4
α-helix	153-159	7
α-helix	160-162	3
α-helix	166-169	4
α-helix	170-180	11
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	243-248	6
α-helix	252-263	12
β-strand	265	1	2
α-helix	272-273	2
β-strand	274	1	2
α-helix	275	1
α-helix	277-285	9
α-helix	290-297	8
α-helix	302-308	7
α-helix	311-313	3
α-helix	320-323	4
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	3
α-helix	368-370	3
α-helix	371-378	8
α-helix	384-394	11
α-helix	403-415	13
α-helix	416-417	2
β-strand	418-419	2	3
α-helix	420-427	8
α-helix	429-451	23
α-helix	453-454	2
α-helix	461-481	21
β-strand	484-485	2	3
α-helix	494-507	14
α-helix	509-521	13
α-helix	523-525	3
β-strand	531-533	3	1
α-helix	546-548	3
α-helix	549-552	4
β-strand	554-559	6	1
β-strand	562-567	6	1
α-helix	576-578	3
β-strand	582-583	2	1
β-strand	589-597	9	1
α-helix	601-608	8
α-helix	613-619	7
β-strand	626-628	3	4
β-strand	632	1	5
α-helix	635	1
β-strand	636-638	3	4
α-helix	640-646	7
α-helix	657-662	6
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	1
α-helix	728-737	10
β-strand	741-746	6	1
α-helix	748-750	3
α-helix	757-759	3
α-helix	760-768	9
α-helix	771-775	5
β-strand	780-781	2	1
β-strand	786-790	5	1
β-strand	797-798	2	6
β-strand	805-807	3	7
β-strand	810	1	8
α-helix	816	1
β-strand	817	1	8
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	851-853	3	7
β-strand	859-860	2	6
α-helix	862-864	3
β-strand	868-877	10	1
α-helix	888-897	10
β-strand	904-908	5	9
β-strand	916-920	5	9
β-strand	926-931	6	9
β-strand	934-935	2	10
β-strand	938-939	2	10
α-helix	940-957	18
α-helix	965-986	22
β-strand	989-994	6	9
α-helix	1009-1023	15
β-strand	1026	1	11
β-strand	1043	1	11
α-helix	1047-1049	3
β-strand	1058-1059	2	9
β-strand	1062-1066	5	9
β-strand	1083	1	12
α-helix	1085-1087	3
α-helix	1091-1099	9
β-strand	1103-1106	4	13
β-strand	1113-1118	6	13
α-helix	1123-1125	3
β-strand	1126	1	12
β-strand	1135-1140	6	13
β-strand	1145-1147	3	14
β-strand	1153-1155	3	14
β-strand	1159-1162	4	15
β-strand	1173-1176	4	15
α-helix	1178-1189	12
α-helix	1200-1206	7
α-helix	1209-1222	14
β-strand	1226-1229	4	16
β-strand	1234-1237	4	16
β-strand	1238-1242	5	17
β-strand	1248-1250	3	17
α-helix	1251-1253	3
α-helix	1262-1283	22
α-helix	1295-1306	12

Chain E: 76 helices, 52 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	8	1	18
β-strand	13-23	11	19
α-helix	27-34	8
α-helix	36-66	31
α-helix	74-86	13
α-helix	89-111	23
α-helix	119-130	12
α-helix	136-139	4
α-helix	141-144	4
α-helix	153-160	8
α-helix	166-169	4
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	237-240	4
α-helix	243-248	6
α-helix	252-263	12
β-strand	265	1	20
α-helix	272-273	2
β-strand	274	1	20
α-helix	275	1
α-helix	277-285	9
α-helix	290-297	8
α-helix	302-308	7
α-helix	311-313	3
α-helix	320-323	4
α-helix	326-342	17
α-helix	345-355	11
α-helix	361-363	3
β-strand	365-366	2	21
α-helix	368-370	3
α-helix	371-378	8
α-helix	384-394	11
α-helix	403-415	13
β-strand	418-419	2	21
α-helix	420-426	7
α-helix	430-451	22
α-helix	453-454	2
α-helix	461-481	21
β-strand	484	1	21
α-helix	494-507	14
α-helix	509-521	13
α-helix	524-526	3
β-strand	531-533	3	19
α-helix	546-548	3
α-helix	549-552	4
β-strand	554-559	6	19
β-strand	562-567	6	19
α-helix	576-578	3
β-strand	582	1	19
β-strand	589-597	9	19
α-helix	601-607	7
α-helix	613-621	9
β-strand	626-628	3	22
β-strand	632	1	23
α-helix	635	1
β-strand	636-638	3	22
α-helix	640-646	7
α-helix	653	1
α-helix	657-662	6
α-helix	666-686	21
β-strand	687	1	23
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	19
α-helix	728-737	10
β-strand	741-746	6	19
α-helix	748-750	3
α-helix	757-759	3
α-helix	760-768	9
α-helix	771-775	5
β-strand	780-781	2	19
β-strand	786-790	5	19
β-strand	798	1	24
β-strand	805-807	3	25
β-strand	810	1	26
β-strand	817	1	26
α-helix	818-819	2
α-helix	820-830	11
α-helix	840-845	6
α-helix	846-848	3
β-strand	851-853	3	25
β-strand	859	1	24
α-helix	862-864	3
β-strand	868-877	10	19
α-helix	888-897	10
β-strand	904-908	5	27
β-strand	916-920	5	27
β-strand	926-931	6	27
β-strand	934-935	2	28
β-strand	938-939	2	28
α-helix	940-957	18
α-helix	965-986	22
β-strand	989-993	5	27
α-helix	1011-1024	14
β-strand	1026	1	18
β-strand	1036	1	29
β-strand	1038	1	29
β-strand	1043	1	18
α-helix	1047-1049	3
α-helix	1052-1054	3
β-strand	1058-1059	2	27
β-strand	1062-1065	4	27
α-helix	1091-1100	10
β-strand	1103-1106	4	30
β-strand	1113-1118	6	30
β-strand	1135-1140	6	30
β-strand	1145-1147	3	31
β-strand	1153-1155	3	31
β-strand	1159-1162	4	32
β-strand	1165	1	33
β-strand	1169	1	33
β-strand	1173-1176	4	32
α-helix	1178-1188	11
α-helix	1200-1203	4
α-helix	1209-1222	14
β-strand	1226-1229	4	34
β-strand	1234-1237	4	34
β-strand	1238-1242	5	35
β-strand	1248-1250	3	35
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, E	protein	1307	Acidaminococcus	U2UMQ6 (AlphaFold model)
Grna (41-mer)	B, F	RNA	44	Acidaminococcus
Ts DNA (31-mer)	C, G	DNA	34	Acidaminococcus
Nts DNA (5'-d(cpapgptpcpcptptptpt)-3')	D, H	DNA	10	Acidaminococcus

Sequence of entity 1 (A, E), FASTA

>9MK3_1 CRISPR-associated endonuclease Cas12a (chains A, E)
MTQFEGFTNLYQVSKTLRFELIPQGKTLKHIQEQGFIEEDKARNDHYKELKPIIDRIYKT
YADQCLQLVQLDWENLSAAIDSYRKEKTEETRNALIEEQATYRNAIHDYFIGRTDNLTDA
INKRHAEIYKGLFKAELFNGKVLKQLGTVTTTEHENALLRSFDKFTTYFSGFYENRKNVF
SAEDISTAIPHRIVQDNFPKFKENCHIFTRLITAVPSLREHFENVKKAIGIFVSTSIEEV
FSFPFYNQLLTQTQIDLYNQLLGGISREAGTEKIKGLNEVLNLAIQKNDETAHIIASLPH
RFIPLFKQILSDRNTLSFILEEFKSDEEVIQSFCKYKTLLRNENVLETAEALFNELNSID
LTHIFISHKKLETISSALCDHWDTLRNALYERRISELTGKITKSAKEKVQRSLKHEDINL
QEIISAAGKELSEAFKQKTSEILSHAHAALDQPLPTTLKKQEEKEILKSQLDSLLGLYHL
LDWFAVDESNEVDPEFSARLTGIKLEMEPSLSFYNKARNYATKKPYSVEKFKLNFQRPTL
ASGWDVNKEKNNGAILFVKNGLYYLGIMPKQKGRYKALSFEPTEKTSEGFDKMYYDYFPD
AAKMIPKCSTQLKAVTAHFQTHTTPILLSNNFIEPLEITKEIYDLNNPEKEPKKFQTAYA
KKTGDQKGYREALCKWIDFTRDFLSKYTKTTSIDLSSLRPSSQYKDLGEYYAELNPLLYH
ISFQRIAEKEIMDAVETGKLYLFQIYNKDFAKGHHGKPNLHTLYWTGLFSPENLAKTSIK
LNGQAELFYRPKSRMKRMAHRLGEKMLNKKLKDQKTPIPDTLYQELYDYVNHRLSHDLSD
EARALLPNVITKEVSHEIIKDRRFTSDKFLFHVPITLNYQAANSPSKFNQRVNAYLKEHP
ETPIIGIDRGERNLIYITVIDSTGKILEQRSLNTIQQFDYQKKLDNREKERVAARQAWSV
VGTIKDLKQGYLSQVIHEIVDLMIHYQAVVVLENLNFGFKSKRTGIAEKAVYQQFEKMLI
DKLNCLVLKDYPAEKVGGVLNPYQLTDQFTSFAKMGTQSGFLFYVPAPYTSKIDPLTGFV
DPFVWKTIKNHESRKHFLEGFDFLHYDVKTGDFILHFKMNRNLSFQRGLPGFMPAWDIVF
EKNETQFDAKGTPFIAGKRIVPVIENHRFTGRYRDLYPANELIALLEEKGIVFRDGSNIL
PKLLENDDSHAIDTMVALIRSVLQMRNSNAATGEDYINSPVRDLNGVCFDSRFQNPEWPM
DADANGAYHIALKGQLLLNHLKESKDLKLQNGISNQDWLAYIQELRN

Sequence of entity 2 (B, F), FASTA

>9MK3_2 gRNA (41-MER) (chains B, F)
UAAUUUCUACUCUUGUAGAUGGAAAUUAGGUGCGCUUGGCAACC

Sequence of entity 3 (C, G), FASTA

>9MK3_3 TS DNA (31-MER) (chains C, G)
GGTTGCCAAGCGCACCTAATTTCCAAAAGGACTG

Sequence of entity 4 (D, H), FASTA

>9MK3_4 NTS DNA (5'-D(*CP*AP*GP*TP*CP*CP*TP*TP*TP*T)-3') (chains D, H)
CAGTCCTTTT

Primary citation

Mechanistic basis for improved activity of Engineered AsCas12a. Jansson-Fritzberg, L., Chica, B., Latrick, C. et al. Commun Biol (2026) 9. DOI 10.1038/s42003-026-09799-1 · 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…
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
8SFI 3.5 Å, WT CRISPR-Cas12a with a 8bp R-loop

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