5XH6: Acidaminococcus sp. BV3L6 Cpf1 RVR variant

Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RVR variant in complex with crRNA and target DNA (TATA PAM). Determined by X-ray diffraction at 2.0 Å resolution. Released 14 Jun 2017.

Method

X-ray diffraction

Resolution

2.0 Å

Organisms

Acidaminococcus sp. (strain BV3L6), Acidaminococcus sp. BV3L6

Chains

4

Atoms

12,831

Mol. weight

180.25 kDa

Released

14 Jun 2017

Explore 5XH6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5XH6 contains 77 α-helices and 52 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: 77 helices, 52 β-strands

Molecules and chains

>5XH6_1 CRISPR-associated endonuclease Cpf1 (chains A)
GSHMTQFEGFTNLYQVSKTLRFELIPQGKTLKHIQEQGFIEEDKARNDHYKELKPIIDRI
YKTYADQCLQLVQLDWENLSAAIDSYRKEKTEETRNALIEEQATYRNAIHDYFIGRTDNL
TDAINKRHAEIYKGLFKAELFNGKVLKQLGTVTTTEHENALLRSFDKFTTYFSGFYENRK
NVFSAEDISTAIPHRIVQDNFPKFKENCHIFTRLITAVPSLREHFENVKKAIGIFVSTSI
EEVFSFPFYNQLLTQTQIDLYNQLLGGISREAGTEKIKGLNEVLNLAIQKNDETAHIIAS
LPHRFIPLFKQILSDRNTLSFILEEFKSDEEVIQSFCKYKTLLRNENVLETAEALFNELN
SIDLTHIFISHKKLETISSALCDHWDTLRNALYERRISELTGKITKSAKEKVQRSLKHED
INLQEIISAAGKELSEAFKQKTSEILSHAHAALDQPLPTTLKKQEEKEILKSQLDSLLGL
YHLLDWFAVDESNEVDPEFSARLTGIKLEMEPSLSFYNKARNYATKKPYSVEKFKLNFQM
PTLARGWDVNVEKNRGAILFVKNGLYYLGIMPKQKGRYKALSFEPTEKTSEGFDKMYYDY
FPDAAKMIPKCSTQLKAVTAHFQTHTTPILLSNNFIEPLEITKEIYDLNNPEKEPKKFQT
AYAKKTGDQKGYREALCKWIDFTRDFLSKYTKTTSIDLSSLRPSSQYKDLGEYYAELNPL
LYHISFQRIAEKEIMDAVETGKLYLFQIYNKDFAKGHHGKPNLHTLYWTGLFSPENLAKT
SIKLNGQAELFYRPKSRMKRMAHRLGEKMLNKKLKDQKTPIPDTLYQELYDYVNHRLSHD
LSDEARALLPNVITKEVSHEIIKDRRFTSDKFFFHVPITLNYQAANSPSKFNQRVNAYLK
EHPETPIIGIDRGERNLIYITVIDSTGKILEQRSLNTIQQFDYQKKLDNREKERVAARQA
WSVVGTIKDLKQGYLSQVIHEIVDLMIHYQAVVVLENLNFGFKSKRTGIAEKAVYQQFEK
MLIDKLNCLVLKDYPAEKVGGVLNPYQLTDQFTSFAKMGTQSGFLFYVPAPYTSKIDPLT
GFVDPFVWKTIKNHESRKHFLEGFDFLHYDVKTGDFILHFKMNRNLSFQRGLPGFMPAWD
IVFEKNETQFDAKGTPFIAGKRIVPVIENHRFTGRYRDLYPANELIALLEEKGIVFRDGS
NILPKLLENDDSHAIDTMVALIRSVLQMRNSNAATGEDYINSPVRDLNGVCFDSRFQNPE
WPMDADANGAYHIALKGQLLLNHLKESKDLKLQNGISNQDWLAYIQELRN

>5XH6_2 crRNA (chains B)
AAUUUCUACUCUUGUAGAUGGAAAUUAGGUGCGCUUGGCAACC

>5XH6_3 Target DNA strand (chains C)
GGTTGCCAAGCGCACCTAATTTCCTATAGGACTG

>5XH6_4 Non-target DNA strand (chains D)
CAGTCCTATA

Primary citation

Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1. Nishimasu, H., Yamano, T., Gao, L. et al. Mol Cell (2017) 67:139-147.e2. DOI 10.1016/j.molcel.2017.04.019 · PubMed

Related structures

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

• 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
• 8SFI 3.5 Å, WT CRISPR-Cas12a with a 8bp R-loop

Browse structure collections

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