8SFI: WT CRISPR-Cas12a with a 8bp R-loop

WT CRISPR-Cas12a with a 8bp R-loop. Determined by electron microscopy at 3.5 Å resolution. Released 3 Jul 2024.

Method

Electron microscopy

Resolution

3.5 Å

Organisms

Acidaminococcus sp. BV3L6, synthetic construct

Chains

4

Atoms

11,477

Mol. weight

201.57 kDa

Released

3 Jul 2024

Explore 8SFI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SFI contains 64 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: 64 helices, 47 β-strands

Molecules and chains

>8SFI_1 CRISPR-associated endonuclease Cas12a (chains A)
GAASMTQFEGFTNLYQVSKTLRFELIPQGKTLKHIQEQGFIEEDKARNDHYKELKPIIDR
IYKTYADQCLQLVQLDWENLSAAIDSYRKEKTEETRNALIEEQATYRNAIHDYFIGRTDN
LTDAINKRHAEIYKGLFKAELFNGKVLKQLGTVTTTEHENALLRSFDKFTTYFSGFYENR
KNVFSAEDISTAIPHRIVQDNFPKFKENCHIFTRLITAVPSLREHFENVKKAIGIFVSTS
IEEVFSFPFYNQLLTQTQIDLYNQLLGGISREAGTEKIKGLNEVLNLAIQKNDETAHIIA
SLPHRFIPLFKQILSDRNTLSFILEEFKSDEEVIQSFCKYKTLLRNENVLETAEALFNEL
NSIDLTHIFISHKKLETISSALCDHWDTLRNALYERRISELTGKITKSAKEKVQRSLKHE
DINLQEIISAAGKELSEAFKQKTSEILSHAHAALDQPLPTTLKKQEEKEILKSQLDSLLG
LYHLLDWFAVDESNEVDPEFSARLTGIKLEMEPSLSFYNKARNYATKKPYSVEKFKLNFQ
MPTLASGWDVNKEKNNGAILFVKNGLYYLGIMPKQKGRYKALSFEPTEKTSEGFDKMYYD
YFPDAAKMIPKCSTQLKAVTAHFQTHTTPILLSNNFIEPLEITKEIYDLNNPEKEPKKFQ
TAYAKKTGDQKGYREALCKWIDFTRDFLSKYTKTTSIDLSSLRPSSQYKDLGEYYAELNP
LLYHISFQRIAEKEIMDAVETGKLYLFQIYNKDFAKGHHGKPNLHTLYWTGLFSPENLAK
TSIKLNGQAELFYRPKSRMKRMAHRLGEKMLNKKLKDQKTPIPDTLYQELYDYVNHRLSH
DLSDEARALLPNVITKEVSHEIIKDRRFTSDKFFFHVPITLNYQAANSPSKFNQRVNAYL
KEHPETPIIGIDRGERNLIYITVIDSTGKILEQRSLNTIQQFDYQKKLDNREKERVAARQ
AWSVVGTIKDLKQGYLSQVIHEIVDLMIHYQAVVVLENLNFGFKSKRTGIAEKAVYQQFE
KMLIDKLNCLVLKDYPAEKVGGVLNPYQLTDQFTSFAKMGTQSGFLFYVPAPYTSKIDPL
TGFVDPFVWKTIKNHESRKHFLEGFDFLHYDVKTGDFILHFKMNRNLSFQRGLPGFMPAW
DIVFEKNETQFDAKGTPFIAGKRIVPVIENHRFTGRYRDLYPANELIALLEEKGIVFRDG
SNILPKLLENDDSHAIDTMVALIRSVLQMRNSNAATGEDYINSPVRDLNGVCFDSRFQNP
EWPMDADANGAYHIALKGQLLLNHLKESKDLKLQNGISNQDWLAYIQELRN

>8SFI_2 RNA (28-MER) (chains B)
UUUUUAAUUUCUACUCUUGUAGAUGUGAUAAGUGGAAUGCCAUGUGGA

>8SFI_3 DNA (5'-D(P*CP*TP*TP*AP*TP*CP*AP*CP*TP*AP*AP*AP*AP*GP*AP*TP*CP*GP*GP*AP*AP*G)-3') (chains C)
AGCACAGTAGCTACTCCAGTACCGTAAGGTCTTATCACTAAAAGATCGGAAGAGCG

>8SFI_4 DNA (5'-D(P*CP*TP*TP*CP*CP*GP*AP*TP*CP*TP*TP*TP*TP*AP*GP*TP*GP*AP*TP*A)-3') (chains D)
CGCTCTTCCGATCTTTTAGTGATAAGACCTTACGGTACTGGAGTAGCTACTGTGCT

Primary citation

Cas12a domain flexibility guides R-loop formation and forces RuvC resetting. Strohkendl, I., Saha, A., Moy, C. et al. Mol Cell (2024) 84:2717-2731.e6. DOI 10.1016/j.molcel.2024.06.007 · PubMed

Related structures

Other PDB entries of the same protein (UniProt U2UMQ6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

• 5XH6 2.0 Å, Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RVR variant in complex with…
• 5XH7 2.0 Å, Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RR variant in complex with crRNA…
• 9MK3 2.7 Å, Engineered AsCas12a (M537R, F870L)
• 5B43 2.8 Å, Crystal structure of Acidaminococcus sp. Cpf1 in complex with crRNA and target DNA
• 22FN 3.17 Å, Cryo-EM structure of AsCas12a in complex with crDNA and RNA target
• 11VQ 3.18 Å, DNA-guided AsCas12a
• 5KK5 3.29 Å, AsCpf1(E993A)-crRNA-DNA ternary complex
• 8SFL 3.3 Å, WT CRISPR-Cas12a with a 15bp R-loop
• 8SFN 3.3 Å, WT CRISPR-Cas12a with a 16bp R-loop and nontarget strand in the RuvC active site.
• 8SFO 3.3 Å, WT CRISPR-Cas12a with a 20bp R-loop and nontarget strand in the RuvC active site.
• 8SFH 3.4 Å, WT CRISPR-Cas12a with a 5bp R-loop
• 9CJI 3.4 Å, Cas12a:gRNA:DNA (Acidaminococcus sp.) with 0 RNA:DNA base pairs, structure 2

Browse structure collections

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