6GTG: CRISPR-associated endonuclease Cas12a

Transition state structure of Cpf1(Cas12a) I4 conformation. Determined by electron microscopy at 3.27 Å resolution. Released 19 Dec 2018.

Method

Electron microscopy

Resolution

3.27 Å

Organism

Francisella tularensis subsp. novicida U112

Chains

4

Atoms

12,538

Mol. weight

203.38 kDa

Ligands

MG

Released

19 Dec 2018

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

Secondary structure: helices and β-sheets

6GTG contains 69 α-helices and 40 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: 69 helices, 40 β-strands

Molecules and chains

>6GTG_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

>6GTG_2 RNA (40-MER) (chains B)
AAUUUCUACUGUUGUAGAUGAGAAGUCAUUUAAUAAGGCCACU

>6GTG_3 DNA (32-MER) (chains C)
ATTGCTTGCTCGATGCATGCAGTGGCCTTATTAAATGACTTCTCTAACGAGCTCG

>6GTG_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

Ligands and cofactors

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

Related structures

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
• 5MGA 3.0 Å, Structure of the Cpf1 endonuclease R-loop complex after DNA cleavage
• 9MKX 3.21 Å, FnoCas12a bridge helix variant state 4b
• 9MKT 3.26 Å, FnoCas12a bridge helix variant state 1
• 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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