11VQ: DNA-guided AsCas12a

DNA-guided AsCas12a. Determined by electron microscopy at 3.18 Å resolution. Released 30 Sept 2026.

Method: Electron microscopy
Resolution: 3.18 Å
Organism: Acidaminococcus sp.
Chains: 3
Atoms: 8,554
Mol. weight: 176.24 kDa
Released: 30 Sept 2026

Explore 11VQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

11VQ contains 59 α-helices and 34 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: 59 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	1
β-strand	13-23	11	2
α-helix	27-34	8
α-helix	36-66	31
α-helix	74-85	12
α-helix	89-111	23
α-helix	119-130	12
α-helix	135-137	3
α-helix	141-146	6
α-helix	153-160	8
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	243-248	6
α-helix	252-263	12
β-strand	264-265	2	3
α-helix	272-273	2
β-strand	274-275	2	3
α-helix	277-285	9
α-helix	290-296	7
α-helix	302-308	7
α-helix	311-313	3
α-helix	320-323	4
α-helix	326-336	11
α-helix	339-342	4
α-helix	345-354	10
α-helix	355-357	3
β-strand	365-366	2	4
α-helix	371-378	8
α-helix	383-390	8
α-helix	391-393	3
α-helix	409-413	5
β-strand	418-419	2	4
α-helix	420-427	8
α-helix	429-451	23
α-helix	461-481	21
β-strand	484	1	4
α-helix	494-521	28
α-helix	524-526	3
β-strand	531-532	2	2
α-helix	546-548	3
α-helix	549-552	4
β-strand	554-559	6	2
β-strand	562-567	6	2
β-strand	571	1	5
β-strand	574	1	5
β-strand	582	1	2
β-strand	589-597	9	2
α-helix	604-605	2
α-helix	606-610	5
α-helix	613-619	7
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	666-684	19
β-strand	687	1	7
α-helix	695-697	3
α-helix	699-700	2
α-helix	701-703	3
α-helix	707-714	8
β-strand	719-727	9	2
α-helix	728-736	9
β-strand	741-746	6	2
α-helix	760-768	9
α-helix	771-775	5
β-strand	779-781	3	2
α-helix	782	1
β-strand	786-790	5	2
β-strand	868-877	10	2
β-strand	882	1	1
α-helix	888-898	11
β-strand	904-908	5	8
β-strand	916-920	5	8
β-strand	926-931	6	8
α-helix	937	1
α-helix	938-942	5
α-helix	943-956	14
α-helix	959-963	5
α-helix	966-986	21
β-strand	989-994	6	8
α-helix	1012-1023	12
β-strand	1026	1	9
β-strand	1043	1	9
β-strand	1046	1	10
β-strand	1058-1059	2	8
β-strand	1060	1	10
β-strand	1062-1066	5	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cas12a	A	protein	1307	Acidaminococcus sp.	U2UMQ6 (AlphaFold model)
Target RNA	B	RNA	38	Acidaminococcus sp.
psiDNA	C	DNA	41	Acidaminococcus sp.

Sequence of entity 1 (A), FASTA

>11VQ_1 CRISPR-associated endonuclease Cas12a (chains A)
MTQFEGFTNLYQVSKTLRFELIPQGKTLKHIQEQGFIEEDKARNDHYKELKPIIDRIYKT
YADQCLQLVQLDWENLSAAIDSYRKEKTEETRNALIEEQATYRNAIHDYFIGRTDNLTDA
INKRHAEIYKGLFKAELFNGKVLKQLGTVTTTEHENALLRSFDKFTTYFSGFYENRKNVF
SAEDISTAIPHRIVQDNFPKFKENCHIFTRLITAVPSLREHFENVKKAIGIFVSTSIEEV
FSFPFYNQLLTQTQIDLYNQLLGGISREAGTEKIKGLNEVLNLAIQKNDETAHIIASLPH
RFIPLFKQILSDRNTLSFILEEFKSDEEVIQSFCKYKTLLRNENVLETAEALFNELNSID
LTHIFISHKKLETISSALCDHWDTLRNALYERRISELTGKITKSAKEKVQRSLKHEDINL
QEIISAAGKELSEAFKQKTSEILSHAHAALDQPLPTTLKKQEEKEILKSQLDSLLGLYHL
LDWFAVDESNEVDPEFSARLTGIKLEMEPSLSFYNKARNYATKKPYSVEKFKLNFQMPTL
ASGWDVNKEKNNGAILFVKNGLYYLGIMPKQKGRYKALSFEPTEKTSEGFDKMYYDYFPD
AAKMIPKCSTQLKAVTAHFQTHTTPILLSNNFIEPLEITKEIYDLNNPEKEPKKFQTAYA
KKTGDQKGYREALCKWIDFTRDFLSKYTKTTSIDLSSLRPSSQYKDLGEYYAELNPLLYH
ISFQRIAEKEIMDAVETGKLYLFQIYNKDFAKGHHGKPNLHTLYWTGLFSPENLAKTSIK
LNGQAELFYRPKSRMKRMAHRLGEKMLNKKLKDQKTPIPDTLYQELYDYVNHRLSHDLSD
EARALLPNVITKEVSHEIIKDRRFTSDKFFFHVPITLNYQAANSPSKFNQRVNAYLKEHP
ETPIIGIDRGERNLIYITVIDSTGKILEQRSLNTIQQFDYQKKLDNREKERVAARQAWSV
VGTIKDLKQGYLSQVIHEIVDLMIHYQAVVVLENLNFGFKSKRTGIAEKAVYQQFEKMLI
DKLNCLVLKDYPAEKVGGVLNPYQLTDQFTSFAKMGTQSGFLFYVPAPYTSKIDPLTGFV
DPFVWKTIKNHESRKHFLEGFDFLHYDVKTGDFILHFKMNRNLSFQRGLPGFMPAWDIVF
EKNETQFDAKGTPFIAGKRIVPVIENHRFTGRYRDLYPANELIALLEEKGIVFRDGSNIL
PKLLENDDSHAIDTMVALIRSVLQMRNSNAATGEDYINSPVRDLNGVCFDSRFQNPEWPM
DADANGAYHIALKGQLLLNHLKESKDLKLQNGISNQDWLAYIQELRN

Sequence of entity 2 (B), FASTA

>11VQ_2 Target RNA (chains B)
GACAUUUAACAACACCAGUCGAUGGGCUGUAGCAUAAA

Sequence of entity 3 (C), FASTA

>11VQ_3 psiDNA (chains C)
ACAGCCCATCGACTGGTGTTTAGATGTGAATCATCTTTAAT

Primary citation

An intricately folded guide RNA scaffold enables DNA targeting by the compact Cas9d nuclease. Fregoso Ocampo, R., Bravo, J., Das, A. et al. To be published.

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
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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