6GTF: CRISPR-associated endonuclease Cas12a

Transient state structure of CRISPR-Cpf1 (Cas12a) I5 conformation. Determined by electron microscopy at 3.63 Å resolution. Released 19 Dec 2018.

Method
Electron microscopy
Resolution
3.63 Å
Organism
Francisella tularensis subsp. novicida U112
Chains
4
Atoms
10,871
Mol. weight
203.28 kDa
Released
19 Dec 2018

Explore 6GTF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GTF contains 65 α-helices and 37 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: 65 helices, 37 β-strands

ElementResiduesLengthSheet
β-strand811
β-strand16-2382
α-helix27-348
α-helix46-516
α-helix57-604
α-helix62-643
α-helix75-8814
α-helix92-11322
α-helix120-1223
α-helix125-1284
α-helix1391
α-helix140-1456
α-helix146-1483
α-helix166-1705
α-helix183-1864
α-helix200-2034
α-helix218-2214
α-helix269-2713
β-strand28813
β-strand29713
α-helix300-3023
α-helix314-3185
α-helix320-3245
α-helix326-3272
α-helix330-3323
α-helix347-35812
α-helix371-3744
α-helix377-3815
β-strand39314
α-helix398-4014
α-helix417-4193
β-strand45114
α-helix453-46513
α-helix477-4804
α-helix488-4925
α-helix493-4953
α-helix498-5014
α-helix504-5063
α-helix520-5234
α-helix524-5274
α-helix532-5354
α-helix540-5434
α-helix562-57110
β-strand596-59832
β-strand61012
α-helix611-6133
α-helix614-6174
β-strand619-62352
β-strand629-63242
α-helix635-6373
α-helix643-6486
β-strand655-66172
α-helix669-6724
α-helix679-6824
α-helix686-6949
α-helix701-7044
α-helix715-72713
α-helix751-7544
α-helix756-7594
β-strand762-76872
α-helix771-7788
β-strand784-78962
α-helix808-8114
β-strand82215
β-strand830-83232
α-helix838-8392
β-strand878-88362
β-strand88615
α-helix888-8903
α-helix899-9068
β-strand912-91326
β-strand927-92827
β-strand92916
β-strand937-93827
β-strand94418
β-strand95118
α-helix953-9553
α-helix956-9616
α-helix977-99822
β-strand1001-100226
β-strand100319
α-helix1026-10327
β-strand103811
α-helix10441
β-strand105511
β-strand1070110
β-strand107419
β-strand1075110
α-helix1103-11097
β-strand1114111
β-strand1117-1118212
β-strand1123-1124212
β-strand1125-1129511
β-strand1141-1145511
α-helix1171-118010
α-helix1192-11965
α-helix1201-121111
β-strand1230113
β-strand1242113
α-helix1258-127417
α-helix1288-12947
α-helix1295-12973

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
CRISPR-associated endonuclease Cas12aAprotein1329Francisella tularensis subsp. novicida U112A0Q7Q2 (AlphaFold model)
RNA (29-mer)BRNA43Francisella tularensis subsp. novicida U112
DNA (5'-d(p*ap*tp*gp*ap*cp*tp*tp*cp*tp*cp*tp*ap*ap*cp*ap*ap*gp*cp*tp*cp*g)-3')CDNA55Francisella tularensis subsp. novicida U112
DNA (5'-d(p*cp*gp*ap*gp*cp*tp*cp*gp*tp*tp*ap*gp*ap*gp*ap*a)-3')DDNA55Francisella tularensis subsp. novicida U112
Sequence of entity 1 (A), FASTA
>6GTF_1 CRISPR-associated endonuclease Cas12a (chains A)
MSIYQEFVNKYSLSKTLRFELIPQGKTLENIKARGLILDDEKRAKDYKKAKQIIDKYHQF
FIEEILSSVCISEDLLQNYSDVYFKLKKSDDDNLQKDFKSAKDTIKKQISEYIKDSEKFK
NLFNQNLIDAKKGQESDLILWLKQSKDNGIELFKANSDITDIDEALEIIKSFKGWTTYFK
GFHENRKNVYSSNDIPTSIIYRIVDDNLPKFLENKAKYESLKDKAPEAINYEQIKKDLAE
ELTFDIDYKTSEVNQRVFSLDEVFEIANFNNYLNQSGITKFNTIIGGKFVNGENTKRKGI
NEYINLYSQQINDKTLKKYKMSVLFKQILSDTESKSFVIDKLEDDSDVVTTMQSFYEQIA
AFKTVEEKSIKETLSLLFDDLKAQKLDLSKIYFKNDKSLTDLSQQVFDDYSVIGTAVLEY
ITQQIAPKNLDNPSKKEQELIAKKTEKAKYLSLETIKLALEEFNKHRDIDKQCRFEEILA
NFAAIPMIFDEIAQNKDNLAQISIKYQNQGKKDLLQASAEDDVKAIKDLLDQTNNLLHKL
KIFHISQSEDKANILDKDEHFYLVFEECYFELANIVPLYNKIRNYITQKPYSDEKFKLNF
ENSTLANGWDKNKEPDNTAILFIKDDKYYLGVMNKKNNKIFDDKAIKENKGEGYKKIVYK
LLPGANKMLPKVFFSAKSIKFYNPSEDILRIRNHSTHTKNGSPQKGYEKFEFNIEDCRKF
IDFYKQSISKHPEWKDFGFRFSDTQRYNSIDEFYREVENQGYKLTFENISESYIDSVVNQ
GKLYLFQIYNKDFSAYSKGRPNLHTLYWKALFDERNLQDVVYKLNGEAELFYRKQSIPKK
ITHPAKEAIANKNKDNPKKESVFEYDLIKDKRFTEDKFFFHCPITINFKSSGANKFNDEI
NLLLKEKANDVHILSIDRGERHLAYYTLVDGKGNIIKQDTFNIIGNDRMKTNYHDKLAAI
EKDRDSARKDWKKINNIKEMKEGYLSQVVHEIAKLVIEYNAIVVFQDLNFGFKRGRFKVE
KQVYQKLEKMLIEKLNYLVFKDNEFDKTGGVLRAYQLTAPFETFKKMGKQTGIIYYVPAG
FTSKICPVTGFVNQLYPKYESVSKSQEFFSKFDKICYNLDKGYFEFSFDYKNFGDKAAKG
KWTIASFGSRLINFRNSDKNHNWDTREVYPTKELEKLLKDYSIEYGHGECIKAAICGESD
KKFFAKLTSVLNTILQMRNSKTGTELDYLISPVADVNGNFFDSRQAPKNMPQDADANGAY
HIGLKGLMLLGRIKNNQEGKKLNLVIKNEEYFEFVQNRNNGSEFELENLYFQGELRRQAS
ALEHHHHHH
Sequence of entity 2 (B), FASTA
>6GTF_2 RNA (29-MER) (chains B)
AAUUUCUACUGUUGUAGAUGAGAAGUCAUUUAAUAAGGCCACU
Sequence of entity 3 (C), FASTA
>6GTF_3 DNA (5'-D(P*AP*TP*GP*AP*CP*TP*TP*CP*TP*CP*TP*AP*AP*CP*AP*AP*GP*CP*TP*CP*G)-3') (chains C)
ATTGCTTGCTCGATGCATGCAGTGGCCTTATTAAATGACTTCTCTAACGAGCTCG
Sequence of entity 4 (D), FASTA
>6GTF_4 DNA (5'-D(P*CP*GP*AP*GP*CP*TP*CP*GP*TP*TP*AP*GP*AP*GP*AP*A)-3') (chains D)
CGAGCTCGTTAGAGAAGTCATTTAATAAGGCCACTGCATGCATCGAGCAAGCAAT

Primary citation

Conformational Activation Promotes CRISPR-Cas12a Catalysis and Resetting of the Endonuclease Activity. Stella, S., Mesa, P., Thomsen, J. et al. Cell (2018) 175:1856-1871.e21. DOI 10.1016/j.cell.2018.10.045 · PubMed

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

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