5NFV: Catalytically inactive FnCas12 mutant

Crystal structure of catalytically inactive FnCas12 mutant bound to an R-loop structure containing a pre-crRNA mimic and full-length DNA target. Determined by X-ray diffraction at 2.5 Å resolution. Released 14 Jun 2017.

Method

X-ray diffraction

Resolution

2.5 Å

Organisms

Francisella tularensis subsp. novicida (strain U112), synthetic construct

Chains

4

Atoms

12,547

Mol. weight

190.5 kDa

Ligands

B3P, MG

Released

14 Jun 2017

Explore 5NFV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NFV contains 74 α-helices and 47 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: 74 helices, 47 β-strands

Molecules and chains

>5NFV_1 CRISPR-associated endonuclease Cpf1 (chains A)
SNASIYQEFVNKYSLSKTLRFELIPQGKTLENIKARGLILDDEKRAKDYKKAKQIIDKYH
QFFIEEILSSVCISEDLLQNYSDVYFKLKKSDDDNLQKDFKSAKDTIKKQISEYIKDSEK
FKNLFNQNLIDAKKGQESDLILWLKQSKDNGIELFKANSDITDIDEALEIIKSFKGWTTY
FKGFHENRKNVYSSNDIPTSIIYRIVDDNLPKFLENKAKYESLKDKAPEAINYEQIKKDL
AEELTFDIDYKTSEVNQRVFSLDEVFEIANFNNYLNQSGITKFNTIIGGKFVNGENTKRK
GINEYINLYSQQINDKTLKKYKMSVLFKQILSDTESKSFVIDKLEDDSDVVTTMQSFYEQ
IAAFKTVEEKSIKETLSLLFDDLKAQKLDLSKIYFKNDKSLTDLSQQVFDDYSVIGTAVL
EYITQQIAPKNLDNPSKKEQELIAKKTEKAKYLSLETIKLALEEFNKHRDIDKQCRFEEI
LANFAAIPMIFDEIAQNKDNLAQISIKYQNQGKKDLLQASAEDDVKAIKDLLDQTNNLLH
KLKIFHISQSEDKANILDKDEHFYLVFEECYFELANIVPLYNKIRNYITQKPYSDEKFKL
NFENSTLANGWDKNKEPDNTAILFIKDDKYYLGVMNKKNNKIFDDKAIKENKGEGYKKIV
YKLLPGANKMLPKVFFSAKSIKFYNPSEDILRIRNHSTHTKNGSPQKGYEKFEFNIEDCR
KFIDFYKQSISKHPEWKDFGFRFSDTQRYNSIDEFYREVENQGYKLTFENISESYIDSVV
NQGKLYLFQIYNKDFSAYSKGRPNLHTLYWKALFDERNLQDVVYKLNGEAELFYRKQSIP
KKITHPAKEAIANKNKDNPKKESVFEYDLIKDKRFTEDKFFFHCPITINFKSSGANKFND
EINLLLKEKANDVHILSIDRGERHLAYYTLVDGKGNIIKQDTFNIIGNDRMKTNYHDKLA
AIEKDRDSARKDWKKINNIKEMKEGYLSQVVHEIAKLVIEYNAIVVFQDLNFGFKRGRFK
VEKQVYQKLEKMLIEKLNYLVFKDNEFDKTGGVLRAYQLTAPFETFKKMGKQTGIIYYVP
AGFTSKICPVTGFVNQLYPKYESVSKSQEFFSKFDKICYNLDKGYFEFSFDYKNFGDKAA
KGKWTIASFGSRLINFRNSDKNHNWDTREVYPTKELEKLLKDYSIEYGHGECIKAAICGE
SDKKFFAKLTSVLNTILQMANSKTGTELDYLISPVADVNGNFFDSRQAPKNMPQDADANG
AYHIGLKGLMLLGRIKNNQEGKKLNLVIKNEEYFEFVQNRNN

>5NFV_2 pre-crRNA (chains B)
AAUAAUUUCUACUGUUGUAGAUAGAUUAAAAGGUAAUUCUAUCUUG

>5NFV_3 DNA target strand (chains C)
ATAGTTCATAGAATTACCTTTTAATCTTAAAGGACTGC

>5NFV_4 DNA non-target strand (chains D)
AGTCCTTTATCTAATTTTCCATTAAGATAGAACTATGC

Ligands and cofactors

Primary citation

Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a. Swarts, D.C., van der Oost, J., Jinek, M. Mol Cell (2017) 66:221-233.e4. DOI 10.1016/j.molcel.2017.03.016 · 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
• 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
• 6GTG 3.27 Å, Transition state structure of Cpf1(Cas12a) I4 conformation
• 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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