6GTD: CRISPR-associated endonuclease Cas12a

Transient state structure of CRISPR-Cpf1 (Cas12a) I2 conformation. Determined by electron microscopy at 4.24 Å resolution. Released 19 Dec 2018.

Method
Electron microscopy
Resolution
4.24 Å
Organisms
Francisella tularensis subsp. novicida (strain U112), Francisella tularensis subsp. novicida U112
Chains
4
Atoms
6,456
Mol. weight
203.28 kDa
Released
19 Dec 2018

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

Secondary structure: helices and β-sheets

6GTD contains 70 α-helices and 42 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: 70 helices, 42 β-strands

ElementResiduesLengthSheet
β-strand811
β-strand2212
α-helix27-348
α-helix37-393
α-helix50-534
α-helix60-634
α-helix73-8715
α-helix96-10813
α-helix110-1134
α-helix118-1203
α-helix137-14812
α-helix162-1643
α-helix165-1706
α-helix199-2013
α-helix208-2147
α-helix219-2235
α-helix231-2344
α-helix240-2423
β-strand243-24423
β-strand256-25723
α-helix258-2592
α-helix282-2854
β-strand287-28824
β-strand297-29824
α-helix301-3055
α-helix306-3116
α-helix357-3615
β-strand363-36425
β-strand368-36925
α-helix370-3723
α-helix373-3775
α-helix381-3833
β-strand392-39436
α-helix397-4004
α-helix402-4076
α-helix410-4134
α-helix414-4174
α-helix422-4254
α-helix439-4424
β-strand450-45236
α-helix4531
α-helix454-4585
α-helix459-4613
α-helix462-4654
α-helix469-4713
α-helix477-4837
α-helix485-4873
α-helix488-4947
α-helix495-4973
α-helix517-5193
α-helix520-5256
α-helix531-5333
α-helix534-5396
α-helix559-5613
α-helix566-5694
α-helix576-5783
β-strand597-59827
β-strand60818
β-strand61818
β-strand62319
β-strand62819
α-helix6321
β-strand633110
α-helix6341
α-helix643-6486
β-strand652111
β-strand657-661512
α-helix669-6713
α-helix676-6783
α-helix686-6894
α-helix714-72916
α-helix734-7374
α-helix750-7534
β-strand762-766512
β-strand769111
α-helix773-7808
β-strand783110
β-strand78712
β-strand822113
β-strand830-83127
β-strand843114
β-strand867114
α-helix872-8743
β-strand886113
α-helix896-9038
β-strand912115
β-strand913116
β-strand916-917216
β-strand925-929516
β-strand935-940616
β-strand943117
β-strand952117
α-helix956-9605
α-helix971-98414
α-helix986-99611
β-strand1001115
β-strand1037118
α-helix10541
β-strand105511
β-strand1056118
α-helix1064-10663
β-strand1071119
β-strand1074119
α-helix1102-111110
β-strand1150-1152320
β-strand1166-1168320
α-helix1175-11784
α-helix1192-11976
α-helix1201-121212
α-helix1262-12665
α-helix1270-12745
α-helix1288-12969

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
CRISPR-associated endonuclease Cas12aAprotein1329Francisella tularensis subsp. novicida (strain U112)A0Q7Q2 (AlphaFold model)
RNA (28-mer)BRNA43Francisella tularensis subsp. novicida U112
DNA (5'-d(p*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*ap*gp*t)-3')DDNA55Francisella tularensis subsp. novicida U112
Sequence of entity 1 (A), FASTA
>6GTD_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
>6GTD_2 RNA (28-MER) (chains B)
AAUUUCUACUGUUGUAGAUGAGAAGUCAUUUAAUAAGGCCACU
Sequence of entity 3 (C), FASTA
>6GTD_3 DNA (5'-D(P*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
>6GTD_4 DNA (5'-D(P*CP*GP*AP*GP*CP*TP*CP*GP*TP*TP*AP*GP*AP*GP*AP*AP*GP*T)-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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