5NG6: FnCas12a

Crystal structure of FnCas12a bound to a crRNA. Determined by X-ray diffraction at 3.34 Å resolution. Released 14 Jun 2017.

Method: X-ray diffraction
Resolution: 3.34 Å
Organisms: Francisella tularensis subsp. novicida (strain U112), synthetic construct
Chains: 8
Atoms: 43,813
Mol. weight: 664.17 kDa
Ligands: MG
Released: 14 Jun 2017

Explore 5NG6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NG6 contains 282 α-helices and 197 β-strands across 4 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: 67 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	1
β-strand	13-23	11	2
α-helix	27-34	8
α-helix	36-68	33
α-helix	73-88	16
α-helix	92-114	23
α-helix	117-120	4
α-helix	125-127	3
α-helix	137-147	11
α-helix	162-171	10
α-helix	176-179	4
α-helix	180-186	7
α-helix	187-190	4
α-helix	199-200	2
α-helix	201-207	7
α-helix	208-224	17
α-helix	231-242	12
β-strand	243-247	5	3
β-strand	252-257	6	3
α-helix	258-259	2
α-helix	260-263	4
α-helix	266-271	6
α-helix	275-286	12
β-strand	288-289	2	4
β-strand	296-297	2	4
α-helix	298	1
α-helix	300-311	12
α-helix	315-319	5
α-helix	322-327	6
α-helix	345-361	17
α-helix	370-383	14
α-helix	388-390	3
β-strand	392-394	3	5
α-helix	397-407	11
α-helix	412-425	14
α-helix	439-444	6
β-strand	450-452	3	5
α-helix	453-465	13
α-helix	475-484	10
α-helix	486-505	20
α-helix	513-515	3
α-helix	520-540	21
β-strand	548	1	6
β-strand	551	1	6
α-helix	559-572	14
α-helix	575-587	13
β-strand	596-598	3	2
β-strand	606	1	7
β-strand	610	1	2
α-helix	614-617	4
β-strand	619-624	6	2
β-strand	627-633	7	2
α-helix	639-641	3
α-helix	643-648	6
β-strand	654-660	7	2
α-helix	665-673	9
α-helix	676-682	7
α-helix	686-694	9
α-helix	702-704	3
α-helix	714-730	17
α-helix	734-737	4
α-helix	744-746	3
α-helix	750-759	10
β-strand	763-769	7	2
α-helix	771-779	9
β-strand	783-789	7	2
α-helix	791-793	3
α-helix	800-802	3
α-helix	803-811	9
α-helix	814-818	5
β-strand	822-824	3	2
β-strand	828	1	7
β-strand	829-833	5	2
β-strand	843	1	8
β-strand	849-850	2	9
β-strand	860-861	2	9
β-strand	867	1	8
α-helix	871-873	3
β-strand	877-886	10	2
α-helix	896-907	12
β-strand	912-917	6	10
β-strand	925-929	5	10
β-strand	935-940	6	10
β-strand	943-945	3	11
β-strand	950-952	3	11
α-helix	953-960	8
α-helix	971-999	29
β-strand	1001-1006	6	10
α-helix	1021-1036	16
β-strand	1038	1	1
β-strand	1048	1	12
β-strand	1053	1	12
β-strand	1055	1	1
α-helix	1059-1061	3
α-helix	1064-1067	4
β-strand	1070-1071	2	10
β-strand	1074-1077	4	10
α-helix	1102-1110	9
β-strand	1114-1118	5	13
β-strand	1123-1127	5	13
β-strand	1129	1	14
β-strand	1141	1	14
β-strand	1144-1145	2	13
β-strand	1150-1152	3	15
α-helix	1163-1165	3
β-strand	1166-1168	3	15
α-helix	1170-1180	11
α-helix	1192-1197	6
α-helix	1201-1215	15
β-strand	1218-1221	4	16
β-strand	1226-1229	4	16
β-strand	1230	1	17
α-helix	1239-1241	3
β-strand	1242	1	17
α-helix	1254-1275	22
α-helix	1288-1297	10

Chain C: 78 helices, 51 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	8	1	18
β-strand	13-23	11	19
α-helix	27-34	8
α-helix	36-68	33
α-helix	73-88	16
α-helix	92-114	23
α-helix	117-120	4
α-helix	125-127	3
α-helix	130	1
β-strand	131	1	20
β-strand	134	1	20
α-helix	135-136	2
α-helix	137-147	11
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	199-201	3
α-helix	202-207	6
α-helix	208-224	17
α-helix	231-242	12
β-strand	243-247	5	21
β-strand	252-257	6	21
α-helix	258-259	2
α-helix	260-263	4
α-helix	266-271	6
α-helix	275-286	12
β-strand	288-289	2	22
β-strand	296-297	2	22
α-helix	298	1
α-helix	300-311	12
α-helix	315-319	5
α-helix	322-327	6
α-helix	345-361	17
α-helix	370-382	13
α-helix	388-390	3
β-strand	392-394	3	23
α-helix	397-407	11
α-helix	412-425	14
α-helix	439-441	3
α-helix	442-446	5
β-strand	450-452	3	23
α-helix	453-464	12
α-helix	475-484	10
α-helix	487-505	19
α-helix	513-515	3
α-helix	517-519	3
α-helix	520-540	21
α-helix	541-543	3
β-strand	548	1	24
β-strand	551	1	24
α-helix	559-572	14
α-helix	575-587	13
β-strand	596-598	3	19
β-strand	606	1	25
β-strand	610	1	19
α-helix	614-617	4
β-strand	619-624	6	19
β-strand	627-633	7	19
α-helix	635-637	3
α-helix	639-641	3
α-helix	643-648	6
β-strand	655-660	6	19
α-helix	665-673	9
α-helix	677-682	6
α-helix	686-694	9
α-helix	702-704	3
α-helix	714-730	17
α-helix	734-737	4
α-helix	741-743	3
α-helix	744-746	3
α-helix	750-761	12
β-strand	763-768	6	19
α-helix	771-779	9
β-strand	783-789	7	19
α-helix	791-793	3
α-helix	800-802	3
α-helix	803-811	9
α-helix	814-818	5
β-strand	822-824	3	19
β-strand	828	1	25
β-strand	829-833	5	19
β-strand	843	1	26
β-strand	849-850	2	27
β-strand	860-861	2	27
β-strand	867	1	26
α-helix	871-873	3
β-strand	877-886	10	19
α-helix	891-893	3
α-helix	896-907	12
β-strand	912-917	6	28
β-strand	925-929	5	28
β-strand	935-940	6	28
β-strand	943-945	3	29
β-strand	950-952	3	29
α-helix	953-960	8
α-helix	971-999	29
β-strand	1001-1006	6	28
α-helix	1021-1036	16
β-strand	1038	1	18
β-strand	1048	1	30
β-strand	1053	1	30
β-strand	1055	1	18
α-helix	1059-1061	3
α-helix	1065-1067	3
β-strand	1070-1071	2	28
β-strand	1074-1077	4	28
α-helix	1102-1110	9
β-strand	1114-1118	5	31
β-strand	1123-1127	5	31
β-strand	1129	1	32
β-strand	1141	1	32
β-strand	1144-1145	2	31
β-strand	1150-1152	3	33
α-helix	1163-1165	3
β-strand	1166-1168	3	33
α-helix	1170-1180	11
α-helix	1192-1197	6
α-helix	1201-1215	15
β-strand	1218-1221	4	34
β-strand	1226-1229	4	34
β-strand	1230-1234	5	35
α-helix	1239	1
β-strand	1240-1242	3	35
α-helix	1254-1274	21
α-helix	1280-1282	3
α-helix	1288-1297	10

Chain E: 69 helices, 49 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	8	1	36
β-strand	13-23	11	37
α-helix	27-34	8
α-helix	36-68	33
α-helix	73-88	16
α-helix	92-113	22
α-helix	117-120	4
α-helix	125-127	3
β-strand	131	1	38
β-strand	134	1	38
α-helix	135-136	2
α-helix	137-147	11
α-helix	162-171	10
α-helix	176-179	4
α-helix	180-187	8
α-helix	188-190	3
α-helix	199-200	2
α-helix	201-207	7
α-helix	208-224	17
α-helix	231-237	7
α-helix	239-242	4
β-strand	244-247	4	39
β-strand	252-256	5	39
α-helix	260-263	4
α-helix	266-271	6
α-helix	275-286	12
β-strand	288	1	40
α-helix	296	1
β-strand	297	1	40
α-helix	298	1
α-helix	300-311	12
α-helix	316-319	4
α-helix	322-327	6
α-helix	345-361	17
α-helix	370-382	13
β-strand	392-394	3	41
α-helix	397-407	11
α-helix	411-425	15
α-helix	439-444	6
β-strand	450-452	3	41
α-helix	453-464	12
α-helix	475-484	10
α-helix	487-505	19
α-helix	513-515	3
α-helix	517-519	3
α-helix	520-540	21
α-helix	559-572	14
α-helix	575-587	13
β-strand	596-598	3	37
β-strand	606	1	42
β-strand	610	1	37
α-helix	614-617	4
β-strand	619-624	6	37
β-strand	627-633	7	37
α-helix	643-649	7
β-strand	654-660	7	37
α-helix	665-673	9
α-helix	678-682	5
α-helix	686-694	9
α-helix	702-704	3
α-helix	714-730	17
α-helix	734-737	4
α-helix	741-743	3
α-helix	750-759	10
β-strand	763-769	7	37
α-helix	771-779	9
β-strand	783-789	7	37
α-helix	791-793	3
α-helix	800-802	3
α-helix	803-811	9
α-helix	814-818	5
β-strand	823-824	2	37
β-strand	828	1	42
β-strand	829-833	5	37
β-strand	843	1	43
β-strand	849-850	2	44
β-strand	860-861	2	44
β-strand	867	1	43
α-helix	871-873	3
β-strand	877-886	10	37
α-helix	896-907	12
β-strand	912-917	6	45
β-strand	925-929	5	45
β-strand	935-940	6	45
β-strand	943-944	2	46
β-strand	951-952	2	46
α-helix	953-960	8
α-helix	971-999	29
β-strand	1001-1006	6	45
α-helix	1021-1036	16
β-strand	1038	1	36
β-strand	1048	1	47
β-strand	1053	1	47
β-strand	1055	1	36
α-helix	1059-1061	3
α-helix	1065-1067	3
β-strand	1070-1071	2	45
β-strand	1074-1077	4	45
α-helix	1102-1111	10
β-strand	1114-1118	5	48
β-strand	1123-1127	5	48
β-strand	1129	1	49
β-strand	1141	1	49
β-strand	1144-1145	2	48
β-strand	1150-1152	3	50
α-helix	1163-1165	3
β-strand	1166-1168	3	50
α-helix	1170-1180	11
α-helix	1192-1195	4
α-helix	1202-1215	14
β-strand	1218-1221	4	51
β-strand	1226-1229	4	51
β-strand	1230	1	52
α-helix	1239-1241	3
β-strand	1242	1	52
α-helix	1254-1275	22
α-helix	1288-1297	10

Chain G: 68 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	53
β-strand	13-23	11	54
α-helix	27-34	8
α-helix	36-68	33
α-helix	73-88	16
α-helix	92-114	23
α-helix	117-120	4
α-helix	125-127	3
α-helix	135-136	2
α-helix	137-147	11
α-helix	162-171	10
α-helix	176-179	4
α-helix	180-187	8
α-helix	188-190	3
α-helix	199-200	2
α-helix	201-207	7
α-helix	208-224	17
α-helix	231-242	12
β-strand	244-246	3	55
β-strand	253-256	4	55
α-helix	260-263	4
α-helix	266-271	6
α-helix	275-286	12
β-strand	288	1	56
α-helix	296	1
β-strand	297	1	56
α-helix	298	1
α-helix	300-311	12
α-helix	315-319	5
α-helix	322-327	6
α-helix	345-361	17
α-helix	370-383	14
α-helix	388-390	3
β-strand	392-394	3	57
α-helix	397-407	11
α-helix	412-421	10
α-helix	440-444	5
β-strand	450-452	3	57
α-helix	453-464	12
α-helix	475-484	10
α-helix	486-506	21
α-helix	513-515	3
α-helix	520-541	22
β-strand	548	1	58
β-strand	551	1	58
α-helix	559-572	14
α-helix	575-587	13
β-strand	596-598	3	54
β-strand	606	1	59
β-strand	610	1	54
α-helix	614-617	4
β-strand	619-624	6	54
β-strand	627-633	7	54
α-helix	643-649	7
β-strand	654-660	7	54
α-helix	665-673	9
α-helix	677-682	6
α-helix	686-694	9
α-helix	702-704	3
α-helix	714-730	17
α-helix	734-737	4
α-helix	741-743	3
α-helix	744-746	3
α-helix	750-761	12
β-strand	763-769	7	54
α-helix	771-779	9
β-strand	783-789	7	54
α-helix	791-793	3
α-helix	800-802	3
α-helix	803-811	9
α-helix	814-818	5
β-strand	822-824	3	54
β-strand	828	1	59
β-strand	829-833	5	54
β-strand	841-843	3	60
β-strand	849-850	2	61
β-strand	860-861	2	61
β-strand	867-868	2	60
α-helix	871-873	3
β-strand	877-886	10	54
α-helix	891-893	3
α-helix	896-907	12
β-strand	912-917	6	62
β-strand	925-929	5	62
β-strand	935-940	6	62
β-strand	943-945	3	63
β-strand	950-952	3	63
α-helix	953-960	8
α-helix	971-999	29
β-strand	1001-1006	6	62
α-helix	1021-1036	16
β-strand	1038	1	53
β-strand	1055	1	53
α-helix	1059-1061	3
α-helix	1065-1067	3
β-strand	1070-1071	2	62
β-strand	1074-1077	4	62
α-helix	1102-1110	9
β-strand	1114-1117	4	64
β-strand	1124-1127	4	64
β-strand	1129	1	65
β-strand	1141	1	65
β-strand	1144-1145	2	64
β-strand	1150-1151	2	66
β-strand	1167-1168	2	66
α-helix	1170-1180	11
β-strand	1190	1	64
α-helix	1192-1197	6
α-helix	1201-1215	15
β-strand	1218-1220	3	67
β-strand	1227-1229	3	67
β-strand	1230	1	68
α-helix	1239-1241	3
β-strand	1242	1	68
α-helix	1254-1275	22
α-helix	1288-1297	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cpf1	A, C, E, G	protein	1302	Francisella tularensis subsp. novicida (strain U112)	A0Q7Q2 (AlphaFold model)
crRNA	B, D, F, H	RNA	43	synthetic construct

Sequence of entity 1 (A, C, E, G), FASTA

>5NG6_1 CRISPR-associated endonuclease Cpf1 (chains A, C, E, G)
SNASIYQEFVNKYSLSKTLRFELIPQGKTLENIKARGLILDDEKRAKDYKKAKQIIDKYH
QFFIEEILSSVCISEDLLQNYSDVYFKLKKSDDDNLQKDFKSAKDTIKKQISEYIKDSEK
FKNLFNQNLIDAKKGQESDLILWLKQSKDNGIELFKANSDITDIDEALEIIKSFKGWTTY
FKGFHENRKNVYSSNDIPTSIIYRIVDDNLPKFLENKAKYESLKDKAPEAINYEQIKKDL
AEELTFDIDYKTSEVNQRVFSLDEVFEIANFNNYLNQSGITKFNTIIGGKFVNGENTKRK
GINEYINLYSQQINDKTLKKYKMSVLFKQILSDTESKSFVIDKLEDDSDVVTTMQSFYEQ
IAAFKTVEEKSIKETLSLLFDDLKAQKLDLSKIYFKNDKSLTDLSQQVFDDYSVIGTAVL
EYITQQIAPKNLDNPSKKEQELIAKKTEKAKYLSLETIKLALEEFNKHRDIDKQCRFEEI
LANFAAIPMIFDEIAQNKDNLAQISIKYQNQGKKDLLQASAEDDVKAIKDLLDQTNNLLH
KLKIFHISQSEDKANILDKDEHFYLVFEECYFELANIVPLYNKIRNYITQKPYSDEKFKL
NFENSTLANGWDKNKEPDNTAILFIKDDKYYLGVMNKKNNKIFDDKAIKENKGEGYKKIV
YKLLPGANKMLPKVFFSAKSIKFYNPSEDILRIRNHSTHTKNGSPQKGYEKFEFNIEDCR
KFIDFYKQSISKHPEWKDFGFRFSDTQRYNSIDEFYREVENQGYKLTFENISESYIDSVV
NQGKLYLFQIYNKDFSAYSKGRPNLHTLYWKALFDERNLQDVVYKLNGEAELFYRKQSIP
KKITHPAKEAIANKNKDNPKKESVFEYDLIKDKRFTEDKFFFHCPITINFKSSGANKFND
EINLLLKEKANDVHILSIDRGERHLAYYTLVDGKGNIIKQDTFNIIGNDRMKTNYHDKLA
AIEKDRDSARKDWKKINNIKEMKEGYLSQVVHEIAKLVIEYNAIVVFEDLNFGFKRGRFK
VEKQVYQKLEKMLIEKLNYLVFKDNEFDKTGGVLRAYQLTAPFETFKKMGKQTGIIYYVP
AGFTSKICPVTGFVNQLYPKYESVSKSQEFFSKFDKICYNLDKGYFEFSFDYKNFGDKAA
KGKWTIASFGSRLINFRNSDKNHNWDTREVYPTKELEKLLKDYSIEYGHGECIKAAICGE
SDKKFFAKLTSVLNTILQMRNSKTGTELDYLISPVADVNGNFFDSRQAPKNMPQDADANG
AYHIGLKGLMLLGRIKNNQEGKKLNLVIKNEEYFEFVQNRNN

Sequence of entity 2 (B, D, F, H), FASTA

>5NG6_2 crRNA (chains B, D, F, H)
AAUUUCUACUGUUGUAGAUAGAUUAAAAGGUAAUUCUAUCUUG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	8

Primary citation

Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a. Swarts, D.C., van der Oost, J., Jinek, M. Mol Cell (2017) 66:221-233.e4. DOI 10.1016/j.molcel.2017.03.016 · 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
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

Browse structure collections

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