9MKU: FnoCas12a bridge helix variant state 2

FnoCas12a bridge helix variant state 2. Determined by electron microscopy at 4.0 Å resolution. Released 11 Feb 2026.

Method: Electron microscopy
Resolution: 4.0 Å
Organisms: synthetic construct, Francisella tularensis subsp. novicida U112
Chains: 3
Atoms: 10,735
Mol. weight: 173.57 kDa
Released: 11 Feb 2026

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

Secondary structure: helices and β-sheets

9MKU contains 58 α-helices and 48 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: 58 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	13	1	1
β-strand	16-18	3	2
β-strand	21-23	3	3
α-helix	27-34	8
α-helix	36-65	30
α-helix	66-68	3
α-helix	73-85	13
α-helix	92-115	24
α-helix	117-120	4
α-helix	125-127	3
α-helix	137-147	11
α-helix	162-170	9
α-helix	176-179	4
α-helix	180-187	8
α-helix	199-203	5
α-helix	207-224	18
α-helix	231-237	7
α-helix	240-242	3
β-strand	243-244	2	4
β-strand	247	1	5
β-strand	252	1	5
β-strand	256-257	2	4
α-helix	262-264	3
α-helix	267-273	7
α-helix	275-286	12
β-strand	287-288	2	6
α-helix	296	1
β-strand	297-298	2	6
α-helix	300-310	11
α-helix	345-361	17
β-strand	363	1	7
β-strand	369	1	7
α-helix	370-382	13
β-strand	392-394	3	8
α-helix	399-405	7
α-helix	412-425	14
β-strand	450-452	3	8
α-helix	453-464	12
α-helix	475-483	9
α-helix	486-504	19
α-helix	513-515	3
α-helix	517-519	3
α-helix	520-539	20
α-helix	560-572	13
α-helix	575-585	11
β-strand	597	1	2
α-helix	614-617	4
β-strand	619-624	6	3
β-strand	627-633	7	3
α-helix	643-648	6
β-strand	650-659	10	3
α-helix	668-673	6
α-helix	679-682	4
α-helix	686-693	8
α-helix	714-730	17
α-helix	733-735	3
α-helix	750-753	4
β-strand	764-769	6	3
α-helix	771-780	10
β-strand	783-788	6	3
α-helix	800-802	3
α-helix	803-811	9
α-helix	814-818	5
β-strand	822-824	3	1
β-strand	829-833	5	2
β-strand	843	1	9
β-strand	848-850	3	10
α-helix	851	1
β-strand	860-862	3	10
β-strand	867	1	9
α-helix	871-874	4
β-strand	877-883	7	2
β-strand	884-886	3	1
α-helix	896-906	11
β-strand	912-918	7	11
β-strand	924-929	6	11
β-strand	935-940	6	11
β-strand	944	1	12
β-strand	951	1	12
α-helix	953-963	11
α-helix	978-999	22
β-strand	1001-1006	6	11
α-helix	1019-1035	17
β-strand	1038	1	13
β-strand	1048	1	14
β-strand	1053	1	14
β-strand	1055	1	13
α-helix	1059-1061	3
β-strand	1070-1071	2	11
β-strand	1074-1077	4	11
α-helix	1102-1109	8
β-strand	1114-1118	5	15
β-strand	1123-1129	7	15
β-strand	1141-1145	5	15
β-strand	1150-1153	4	16
β-strand	1165-1168	4	16
α-helix	1170-1180	11
α-helix	1192-1197	6
α-helix	1201-1214	14
β-strand	1218-1219	2	17
β-strand	1228-1229	2	17
β-strand	1230	1	18
β-strand	1242	1	18
α-helix	1254-1274	21
α-helix	1276-1277	2
α-helix	1288-1295	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
crRNA	B	RNA	43	synthetic construct
Ts DNA	C	DNA	24	synthetic construct
CRISPR-associated endonuclease Cas12a	A	protein	1305	Francisella tularensis subsp. novicida U112	A0Q7Q2 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9MKU_1 crRNA (chains B)
AAUUUCUACUGUUGUAGAUGAGAAGUCAUUUAAUAAGGCCACU

Sequence of entity 2 (C), FASTA

>9MKU_2 TS DNA (chains C)
GCCTTATTAAATGACTTCTCTAAA

Sequence of entity 3 (A), FASTA

>9MKU_3 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

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
9MKT 3.26 Å, FnoCas12a bridge helix variant state 1
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

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