5MGA: CRISPR-associated endonuclease Cpf1

Structure of the Cpf1 endonuclease R-loop complex after DNA cleavage. Determined by X-ray diffraction at 3.0 Å resolution. Released 21 Jun 2017.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Francisella tularensis subsp. novicida U112
Chains: 4
Atoms: 11,351
Mol. weight: 179.33 kDa
Ligands: MG
Released: 21 Jun 2017

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

Secondary structure: helices and β-sheets

5MGA contains 61 α-helices and 36 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: 61 helices, 36 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	76-86	11
α-helix	92-115	24
α-helix	125-127	3
α-helix	137-140	4
α-helix	141-148	8
β-strand	156	1	3
β-strand	159	1	3
α-helix	162-170	9
α-helix	176-179	4
α-helix	180-189	10
α-helix	199-201	3
α-helix	202-207	6
α-helix	208-222	15
α-helix	232-237	6
α-helix	266-271	6
α-helix	275-286	12
β-strand	288	1	4
α-helix	296	1
β-strand	297	1	4
α-helix	298	1
α-helix	300-308	9
α-helix	316-319	4
α-helix	323-327	5
α-helix	338-341	4
α-helix	345-361	17
α-helix	372-378	7
α-helix	400-406	7
α-helix	415-419	5
α-helix	460-463	4
α-helix	471-477	7
α-helix	480-490	11
α-helix	494-497	4
α-helix	520-538	19
α-helix	567-572	6
α-helix	575-586	12
β-strand	596-598	3	2
β-strand	610	1	2
α-helix	611-613	3
α-helix	614-617	4
β-strand	619-624	6	2
β-strand	627-633	7	2
α-helix	635-637	3
α-helix	643-648	6
β-strand	650	1	2
β-strand	653-661	9	2
α-helix	665-673	9
α-helix	679-682	4
α-helix	686-692	7
α-helix	714-730	17
α-helix	735-737	3
α-helix	750-760	11
β-strand	762-770	9	2
α-helix	771-779	9
β-strand	783-789	7	2
α-helix	791-793	3
α-helix	800-802	3
α-helix	803-810	8
α-helix	814-818	5
β-strand	822-824	3	2
β-strand	829-833	5	2
β-strand	841	1	5
β-strand	868	1	5
α-helix	871-874	4
β-strand	877-886	10	2
α-helix	896-906	11
β-strand	912-917	6	6
β-strand	925-929	5	6
β-strand	935-940	6	6
α-helix	953-969	17
α-helix	973-976	4
α-helix	978-999	22
β-strand	1001-1006	6	6
α-helix	1024-1036	13
β-strand	1038	1	1
β-strand	1055	1	1
α-helix	1059-1061	3
β-strand	1070-1071	2	6
β-strand	1074-1077	4	6
α-helix	1106-1109	4
β-strand	1115-1118	4	7
β-strand	1123-1128	6	7
β-strand	1142-1144	3	7
α-helix	1170-1180	11
α-helix	1207-1214	8
β-strand	1219	1	8
β-strand	1228	1	8
β-strand	1230	1	9
β-strand	1235	1	10
β-strand	1239	1	10
β-strand	1242	1	9
α-helix	1243-1245	3
α-helix	1254-1274	21
α-helix	1288-1296	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cpf1	A	protein	1323	Francisella tularensis subsp. novicida U112	A0Q7Q2 (AlphaFold model)
RNA (40-mer)	B	RNA	40	Francisella tularensis subsp. novicida U112
DNA (26-mer)	C	DNA	26	Francisella tularensis subsp. novicida U112
DNA (5'-d(pcpgptptpapgpapgpapapgpt)-3')	D	DNA	12	Francisella tularensis subsp. novicida U112

Sequence of entity 1 (A), FASTA

>5MGA_1 CRISPR-associated endonuclease Cpf1 (chains A)
MSIYQEFVNKYSLSKTLRFELIPQGKTLENIKARGLILDDEKRAKDYKKAKQIIDKYHQF
FIEEILSSVCISEDLLQNYSDVYFKLKKSDDDNLQKDFKSAKDTIKKQISEYIKDSEKFK
NLFNQNLIDAKKGQESDLILWLKQSKDNGIELFKANSDITDIDEALEIIKSFKGWTTYFK
GFHENRKNVYSSNDIPTSIIYRIVDDNLPKFLENKAKYESLKDKAPEAINYEQIKKDLAE
ELTFDDDYKTSEVNQRVFSLDEVFEIANFNNYLNQSGITKFNTIIGGKFVNGENTKRKGI
NEYINLYSQQINDKTLKKYKMSVLFKQILSDTESKSFVIDKLEDDSDVVTTMQSFYEQIA
AFKTVEEKSIKETLSLLFDDLKAQKLDLSKIYFKNDKSLTDLSQQVFDDYSVIGTAVLEY
ITQQIAPKNLDNPSKKEQELIAKKTEKAKYLSLETILLALEEFNKHRDIDKQCRFEEILA
NFAAIPMIFDEIAQNKDNLAQISIKYQNQGKKDLLQASAEDDVKAIKDLLDQTNNLLHKL
KIFHISQSEDKANILDKDEHFYLVFEECYFELANIVPLYNKIRNYITQKPYSDEKFKLNF
ENSTLANGWDKNKEPDNTAILFIKDDKYYLGVMNKKNNKIFDDKAIKENKGEGYKKIVYK
LLPGANKMLPKVFFSAKSIKFYNPSEDILRIRNHSTHTKNGSPQKGYEKFEFNIEDCRKF
IDFYKQSISKHPEWKDFGFRFSDTQRYNSIDEFYREVENQGYKLTFENISESYIDSVVNQ
GKLYLFQIYNKDFSAYSKGRPNLHTLYWKALFDERNLQDVVYKLNGEAELFYRKQSIPKK
IIHPAKEAIANKNKDNPKKESVFEYDLIKDKRFTEDKFFFHCPITINFKSSGANKFNDEI
NLLLKEKANDVHILSIDRGERHLAYYTLVDGKGNIIKQDTFNIIGNDRMKTNYHDKLAAI
EKDRDSARKDWKKINNIKEMKEGYLSQVVHEIAKLVIEYNAIVVFEDLNFGFKRGRFKVE
KQVYQKLEKMLIEKLNYLVFKDNEFDKTGGVLRAYQLTAPFETFKKMGKQTGIIYYVPAG
FTSKICPVTGFVNQLYPKYESVSKSQEFFSKFDKICYNLDKGYFEFSFDYKNFGDKAAKG
KWTIASFGSRLINFRNSDKNHNWDTREVYPTKELEKLLKDYSIEYGHGECIKAAICGESD
KKFFAKLTSVLNTILQMRNSKTGTELDYLISPVADVNGNFFDSRQAPKNMPQDADANGAY
HIGLKGLMLLGRIKNNQEGKKLNLVIKNEEYFEFVQNRNNGSEFELENLYFQGELRRQAS
ALE

Sequence of entity 2 (B), FASTA

>5MGA_2 RNA (40-MER) (chains B)
AAUUUCUACUGUUGUAGAUGAGAAGUCAUUUAAUAAGGCC

Sequence of entity 3 (C), FASTA

>5MGA_3 DNA (26-MER) (chains C)
GGCCTTATTAAATGACTTCTCTAACG

Sequence of entity 4 (D), FASTA

>5MGA_4 DNA (5'-D(P*CP*GP*TP*TP*AP*GP*AP*GP*AP*AP*GP*T)-3') (chains D)
CGTTAGAGAAGT

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

Primary citation

Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage. Stella, S., Alcon, P., Montoya, G. Nature (2017) 546:559-563. DOI 10.1038/nature22398 · 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
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
9MKV 3.68 Å, FnoCas12a bridge helix variant state 3

Browse structure collections

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