9MKV: FnoCas12a bridge helix variant state 3

FnoCas12a bridge helix variant state 3. Determined by electron microscopy at 3.68 Å resolution. Released 11 Feb 2026.

Method: Electron microscopy
Resolution: 3.68 Å
Organisms: Francisella tularensis subsp. novicida U112, synthetic construct
Chains: 4
Atoms: 8,481
Mol. weight: 181 kDa
Released: 11 Feb 2026

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

Secondary structure: helices and β-sheets

9MKV contains 44 α-helices and 26 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: 44 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	1
β-strand	13-22	10	2
α-helix	27-34	8
α-helix	40-68	29
α-helix	74-78	5
α-helix	84-88	5
α-helix	94-114	21
α-helix	117-120	4
α-helix	125-127	3
α-helix	137-142	6
α-helix	162-170	9
α-helix	181-189	9
α-helix	199-202	4
α-helix	203-207	5
α-helix	208-221	14
α-helix	233-237	5
α-helix	266-272	7
α-helix	275-286	12
α-helix	300-306	7
α-helix	325-327	3
β-strand	595-596	2	2
α-helix	614-617	4
β-strand	620-624	5	2
β-strand	627-633	7	2
α-helix	644-647	4
β-strand	655-661	7	2
α-helix	669-673	5
α-helix	678-680	3
α-helix	686-691	6
α-helix	715-730	16
α-helix	735-737	3
α-helix	750-758	9
β-strand	762-767	6	2
α-helix	772-780	9
β-strand	783-789	7	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
β-strand	877-886	10	2
α-helix	896-907	12
α-helix	908-910	3
β-strand	912-918	7	3
β-strand	924-929	6	3
β-strand	935-940	6	3
α-helix	979-993	15
α-helix	996-999	4
β-strand	1001-1006	6	3
α-helix	1022-1035	14
β-strand	1038	1	1
α-helix	1044	1
β-strand	1055	1	1
α-helix	1059-1061	3
β-strand	1070-1071	2	3
β-strand	1074-1077	4	3
α-helix	1103-1110	8
β-strand	1115-1116	2	4
β-strand	1125-1127	3	4
β-strand	1143-1144	2	4
β-strand	1150-1151	2	5
β-strand	1167-1168	2	5
α-helix	1170-1180	11
α-helix	1192-1197	6
α-helix	1201-1215	15
β-strand	1230	1	6
β-strand	1242	1	6
α-helix	1243-1245	3
α-helix	1254-1274	21
α-helix	1288-1297	10

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
Ts DNA	C	DNA	24	synthetic construct
Nts DNA	D	DNA	24	synthetic construct

Sequence of entity 1 (A), FASTA

>9MKV_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

>9MKV_2 crRNA (chains B)
AAUUUCUACUGUUGUAGAUGAGAAGUCAUUUAAUAAGGCCACU

Sequence of entity 3 (C), FASTA

>9MKV_3 TS DNA (chains C)
GCCTTATTAAATGACTTCTCTAAA

Sequence of entity 4 (D), FASTA

>9MKV_4 NTS DNA (chains D)
TTTAGAGAAGTCATTTAATAAGGC

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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