6GTC: CRISPR-associated endonuclease Cas12a

Transition state structure of Cpf1(Cas12a) I1 conformation. Determined by electron microscopy at 3.91 Å resolution. Released 19 Dec 2018.

Method
Electron microscopy
Resolution
3.91 Å
Organism
Francisella tularensis subsp. novicida U112
Chains
4
Atoms
11,931
Mol. weight
203.28 kDa
Released
19 Dec 2018

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

Secondary structure: helices and β-sheets

6GTC contains 58 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: 58 helices, 42 β-strands

ElementResiduesLengthSheet
α-helix3-53
β-strand811
β-strand1312
β-strand16-2383
α-helix27-348
α-helix38-436
α-helix46-483
α-helix51-6313
α-helix74-8815
α-helix95-10612
α-helix110-1134
α-helix125-1273
α-helix137-14711
α-helix162-1698
α-helix208-2114
α-helix213-22210
α-helix231-2377
β-strand243-24424
β-strand256-25724
α-helix258-2592
α-helix278-2847
β-strand288-29035
β-strand295-29735
α-helix300-31011
α-helix324-3274
α-helix370-38011
β-strand392-39436
α-helix399-4079
α-helix413-42513
β-strand450-45236
α-helix453-46311
α-helix464-4663
α-helix476-4827
α-helix488-49811
α-helix520-5223
α-helix524-5274
α-helix561-5644
α-helix576-5794
β-strand595-59733
β-strand619-62353
β-strand628-63363
β-strand657-66157
α-helix669-6735
α-helix680-6823
α-helix686-6949
α-helix716-7183
α-helix720-7289
α-helix744-7463
α-helix751-7577
β-strand762-76657
α-helix771-7744
α-helix777-7804
β-strand783-78973
α-helix803-8064
α-helix808-8103
α-helix814-8185
β-strand823-82428
β-strand829-83353
β-strand841-84339
β-strand848110
β-strand862110
β-strand867-86829
α-helix871-8733
β-strand877-88373
β-strand884-88528
β-strand88612
α-helix896-9016
α-helix904-9063
α-helix908-9103
β-strand927-929311
β-strand935-938411
β-strand943-944212
β-strand951-952212
α-helix953-9586
α-helix971-99323
α-helix995-9984
β-strand1003-1006413
α-helix1022-10254
β-strand103811
β-strand105511
α-helix1065-10673
β-strand1070113
β-strand1074-1077413
α-helix1104-11118
β-strand1114-1117414
β-strand1124-1127414
α-helix1130-11323
β-strand1144114
β-strand1150-1153415
β-strand1165-1168415
α-helix1170-117910
α-helix1192-11976
α-helix1201-121111
β-strand1219-1220216
β-strand1227-1228216
β-strand1230117
β-strand1242117
α-helix1243-12453
α-helix1257-127418
α-helix1288-12947

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
CRISPR-associated endonuclease Cas12aAprotein1329Francisella tularensis subsp. novicida U112A0Q7Q2 (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*g)-3')DDNA55Francisella tularensis subsp. novicida U112
Sequence of entity 1 (A), FASTA
>6GTC_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
>6GTC_2 RNA (28-MER) (chains B)
AAUUUCUACUGUUGUAGAUGAGAAGUCAUUUAAUAAGGCCACU
Sequence of entity 3 (C), FASTA
>6GTC_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
>6GTC_4 DNA (5'-D(P*CP*GP*AP*GP*CP*TP*CP*GP*TP*TP*AP*GP*AP*GP*AP*AP*G)-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:

Browse structure collections

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