9MKT: FnoCas12a bridge helix variant state 1

FnoCas12a bridge helix variant state 1. Determined by electron microscopy at 3.26 Å resolution. Released 11 Feb 2026.

Method: Electron microscopy
Resolution: 3.26 Å
Organisms: Francisella tularensis subsp. novicida U112, synthetic construct
Chains: 2
Atoms: 10,866
Mol. weight: 166.26 kDa
Released: 11 Feb 2026

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

Secondary structure: helices and β-sheets

9MKT contains 66 α-helices and 35 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, 35 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	1
β-strand	13-22	10	2
α-helix	27-34	8
α-helix	36-45	10
α-helix	48-65	18
α-helix	76-88	13
α-helix	92-115	24
α-helix	125-128	4
α-helix	137-142	6
α-helix	153-155	3
α-helix	162-171	10
α-helix	176-179	4
α-helix	180-187	8
α-helix	188-190	3
α-helix	199-202	4
α-helix	203-207	5
α-helix	208-224	17
α-helix	234-237	4
α-helix	239-241	3
α-helix	260-263	4
α-helix	266-269	4
α-helix	270-272	3
α-helix	275-286	12
α-helix	296-298	3
α-helix	300-311	12
α-helix	325-327	3
α-helix	347-355	9
β-strand	363	1	3
β-strand	369	1	3
α-helix	370-382	13
β-strand	392-393	2	4
α-helix	397-406	10
α-helix	412-420	9
α-helix	421-425	5
α-helix	437-441	5
α-helix	445-448	4
α-helix	450	1
β-strand	451-452	2	4
α-helix	453-465	13
α-helix	481-495	15
α-helix	500-503	4
α-helix	521-536	16
α-helix	538-540	3
α-helix	565-572	8
α-helix	575-586	12
β-strand	596-597	2	2
β-strand	620-624	5	2
β-strand	627-631	5	2
α-helix	633-634	2
α-helix	644-647	4
β-strand	655-661	7	2
α-helix	665-672	8
α-helix	687-694	8
α-helix	714-730	17
α-helix	732-735	4
α-helix	750-760	11
β-strand	762-768	7	2
α-helix	774-780	7
β-strand	785-789	5	2
α-helix	791-793	3
α-helix	803-810	8
α-helix	814-818	5
β-strand	822-824	3	2
β-strand	829-833	5	2
α-helix	838-839	2
β-strand	841-843	3	5
β-strand	867-868	2	5
β-strand	877-886	10	2
α-helix	896-906	11
β-strand	912-918	7	6
β-strand	924-929	6	6
β-strand	935-940	6	6
β-strand	944-945	2	7
β-strand	950-951	2	7
α-helix	957-960	4
α-helix	977-999	23
β-strand	1001-1006	6	6
α-helix	1007	1
α-helix	1021-1035	15
α-helix	1044	1
β-strand	1055	1	1
α-helix	1065-1067	3
β-strand	1070-1071	2	6
β-strand	1074-1077	4	6
α-helix	1081-1083	3
α-helix	1102-1109	8
β-strand	1114-1118	5	8
β-strand	1123-1129	7	8
β-strand	1141-1145	5	8
β-strand	1150-1152	3	9
β-strand	1166-1168	3	9
α-helix	1170-1179	10
α-helix	1191-1197	7
α-helix	1203-1215	13
β-strand	1218-1219	2	10
β-strand	1228-1229	2	10
β-strand	1230	1	11
β-strand	1242	1	11
α-helix	1243-1245	3
α-helix	1256-1274	19
α-helix	1288-1298	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cas12a	A	protein	1305	Francisella tularensis subsp. novicida U112	A0Q7Q2 (AlphaFold model)
crRNA	B	RNA	43	synthetic construct

Sequence of entity 1 (A), FASTA

>9MKT_1 CRISPR-associated endonuclease Cas12a (chains A)
GAASHMSIYQEFVNKYSLSKTLRFELIPQGKTLENIKARGLILDDEKRAKDYKKAKQIID
KYHQFFIEEILSSVCISEDLLQNYSDVYFKLKKSDDDNLQKDFKSAKDTIKKQISEYIKD
SEKFKNLFNQNLIDAKKGQESDLILWLKQSKDNGIELFKANSDITDIDEALEIIKSFKGW
TTYFKGFHENRKNVYSSNDIPTSIIYRIVDDNLPKFLENKAKYESLKDKAPEAINYEQIK
KDLAEELTFDIDYKTSEVNQRVFSLDEVFEIANFNNYLNQSGITKFNTIIGGKFVNGENT
KRKGINEYINLYSQQINDKTLKKYKMSVLFKQILSDTESKSFVIDKLEDDSDVVTTMQSF
YEQIAAFKTVEEKSIKETLSLLFDDLKAQKLDLSKIYFKNDKSLTDLSQQVFDDYSVIGT
AVLEYITQQIAPKNLDNPSKKEQELIAKKTEKAKYLSLETIKLALEEFNKHRDIDKQCRF
EEILANFAAIPMIFDEIAQNKDNLAQISIKYQNQGKKDLLQASAEDDVKAIKDLLDQTNN
LLHKLKIFHISQSEDKANILDKDEHFYLVFEECYFELANIVPLYNKIRNYITQKPYSDEK
FKLNFENSTLANGWDKNKEPDNTAILFIKDDKYYLGVMNKKNNKIFDDKAIKENKGEGYK
KIVYKLLPGANKMLPKVFFSAKSIKFYNPSEDILRIRNHSTHTKNGSPQKGYEKFEFNIE
DCRKFIDFYKQSISKHPEWKDFGFRFSDTQRYNSIDEFYREVENQGYKLTFENISESYID
SVVNQGKLYLFQIYNKDFSAYSKGRPNLHTLYWKALFDERNLQDVVYKLNGEAELFYRKQ
SIPKKITHPAKEAIANKNKDNPKKESVFEYDLIKDKRFTEDKFFFHCPITINFKSSGANK
FNDEINLLLKEKANDVHILSIDRGERHLAYYTLVDGKGNIIKQDTFNIIGNDRMKTNYHD
KLAAIEKDRDSARPPWKKINNIKEMKEGYLSQVVHEIAKLVIEYNAIVVFEDLNFGFKRG
RFKVEKQVYQKLEKMLIEKLNYLVFKDNEFDKTGGVLRAYQLTAPFETFKKMGKQTGIIY
YVPAGFTSKICPVTGFVNQLYPKYESVSKSQEFFSKFDKICYNLDKGYFEFSFDYKNFGD
KAAKGKWTIASFGSRLINFRNSDKNHNWDTREVYPTKELEKLLKDYSIEYGHGECIKAAI
CGESDKKFFAKLTSVLNTILQMRNSKTGTELDYLISPVADVNGNFFDSRQAPKNMPQDAD
ANGAYHIGLKGLMLLGRIKNNQEGKKLNLVIKNEEYFEFVQNRNN

Sequence of entity 2 (B), FASTA

>9MKT_2 crRNA (chains B)
AAUUUCUACUGUUGUAGAUGAGAAGUCAUUUAAUAAGGCCACU

Primary citation

Bridge helix of Cas12a is an allosteric regulator of R-loop formation and RuvC activation. Ganguly, C., Aribam, S.D., Dos Santos, A.M. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-68657-0 · PubMed

Other PDB entries of the same protein (UniProt A0Q7Q2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8Y0B 2.3 Å, Crystal structure of FnCas12a in complex with pre-crRNA and 12nt target DNA
5NFV 2.5 Å, Crystal structure of catalytically inactive FnCas12 mutant bound to an R-loop structure…
6I1K 2.65 Å, Crystal structure of catalytically inactive FnCas12a in complex with a crRNA guide and a…
6I1L 2.98 Å, Crystal structure of FnCas12a in complex with a crRNA guide and ssDNA target
5MGA 3.0 Å, Structure of the Cpf1 endonuclease R-loop complex after DNA cleavage
9MKX 3.21 Å, FnoCas12a bridge helix variant state 4b
6GTG 3.27 Å, Transition state structure of Cpf1(Cas12a) I4 conformation
5NG6 3.34 Å, Crystal structure of FnCas12a bound to a crRNA
8Y0C 3.45 Å, Crystal structure of FnCas12a in complex with pre-crRNA and 18nt target DNA
6GTF 3.63 Å, Transient state structure of CRISPR-Cpf1 (Cas12a) I5 conformation
9MKW 3.63 Å, FnoCas12a bridge helix variant state 4a
9MKV 3.68 Å, FnoCas12a bridge helix variant state 3

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