6GTE: CRISPR-associated endonuclease Cas12a

Transient state structure of CRISPR-Cpf1 (Cas12a) I3 conformation. Determined by electron microscopy at 4.07 Å resolution. Released 19 Dec 2018.

Method
Electron microscopy
Resolution
4.07 Å
Organisms
Francisella tularensis subsp. novicida (strain U112), Francisella tularensis subsp. novicida U112
Chains
4
Atoms
10,872
Mol. weight
203.28 kDa
Released
19 Dec 2018

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

Secondary structure: helices and β-sheets

6GTE contains 71 α-helices and 41 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: 71 helices, 41 β-strands

ElementResiduesLengthSheet
β-strand811
β-strand17-2372
α-helix27-315
α-helix50-523
α-helix58-625
α-helix76-849
α-helix98-11316
α-helix120-1223
α-helix137-1426
α-helix162-1709
α-helix200-2067
α-helix212-2198
α-helix230-2334
α-helix256-2583
α-helix266-2683
α-helix275-28410
α-helix296-2983
α-helix300-3023
α-helix304-3074
α-helix314-3196
α-helix324-3274
α-helix347-35610
α-helix358-3614
β-strand36313
β-strand36913
α-helix370-3778
α-helix400-4023
α-helix403-4075
α-helix413-4153
α-helix418-4214
α-helix454-4596
α-helix461-4644
α-helix485-49410
α-helix497-4993
α-helix500-5056
α-helix517-5193
α-helix523-5275
α-helix529-5313
α-helix534-5396
α-helix540-5434
α-helix565-5684
α-helix569-5746
α-helix575-5795
α-helix583-5875
β-strand596-59832
α-helix611-6133
α-helix614-6174
β-strand620-62342
β-strand628-63142
α-helix644-6474
β-strand653-65424
β-strand655-65622
β-strand657-66155
α-helix665-6728
α-helix679-6824
α-helix686-6949
α-helix715-72410
α-helix734-7374
α-helix741-7433
α-helix744-7463
α-helix751-7544
β-strand762-76655
β-strand769-77024
α-helix771-78010
β-strand785-78952
α-helix808-8114
β-strand822-82436
β-strand829-83352
α-helix834-8352
β-strand877-88262
β-strand884-88636
α-helix896-9049
β-strand912-91327
β-strand925-92957
β-strand935-94067
β-strand94318
β-strand95218
α-helix954-9607
α-helix980-99819
β-strand1001-100227
β-strand100319
β-strand1006110
α-helix1026-10327
β-strand103811
α-helix10441
β-strand105511
β-strand1070111
β-strand107419
β-strand1075111
β-strand1077110
α-helix1103-11108
β-strand1114112
β-strand1117113
β-strand1124113
β-strand1125-1126214
β-strand1127112
α-helix1130-11323
β-strand1144-1145214
β-strand1150115
β-strand1168115
α-helix1170-11778
α-helix1192-11976
α-helix1201-121212
β-strand1218116
β-strand1229116
α-helix1243-12453
α-helix1257-12604
α-helix1262-12654
α-helix1266-12683
α-helix1269-12735
α-helix1288-12947
α-helix1295-12973

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
CRISPR-associated endonuclease Cas12aAprotein1329Francisella tularensis subsp. novicida (strain U112)A0Q7Q2 (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*ap*g)-3')DDNA55Francisella tularensis subsp. novicida U112
Sequence of entity 1 (A), FASTA
>6GTE_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
>6GTE_2 RNA (29-MER) (chains B)
AAUUUCUACUGUUGUAGAUGAGAAGUCAUUUAAUAAGGCCACU
Sequence of entity 3 (C), FASTA
>6GTE_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
>6GTE_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:

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