5KK5: AsCpf1(E993A)-crRNA-DNA ternary complex

AsCpf1(E993A)-crRNA-DNA ternary complex. Determined by X-ray diffraction at 3.29 Å resolution. Released 10 Aug 2016.

Method: X-ray diffraction
Resolution: 3.29 Å
Organisms: Acidaminococcus sp. (strain BV3L6), Acidaminococcus sp. BV3L6
Chains: 4
Atoms: 11,201
Mol. weight: 178.33 kDa
Released: 10 Aug 2016

Explore 5KK5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KK5 contains 59 α-helices and 45 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: 59 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	1
β-strand	13-23	11	2
α-helix	26-34	9
α-helix	36-68	33
α-helix	74-81	8
α-helix	89-111	23
α-helix	119-132	14
α-helix	136-139	4
α-helix	141-145	5
α-helix	153-159	7
α-helix	166-169	4
α-helix	170-180	11
α-helix	189-191	3
α-helix	192-197	6
α-helix	198-214	17
α-helix	216-229	14
α-helix	237-240	4
α-helix	243-248	6
α-helix	252-263	12
β-strand	264-265	2	3
α-helix	272-273	2
β-strand	274-275	2	3
α-helix	277-286	10
α-helix	290-297	8
α-helix	302-308	7
α-helix	320-323	4
α-helix	326-343	18
α-helix	346-358	13
β-strand	365-366	2	4
α-helix	368-378	11
α-helix	382-395	14
α-helix	403-415	13
β-strand	418-419	2	4
α-helix	420-427	8
α-helix	430-451	22
α-helix	461-482	22
β-strand	484	1	4
α-helix	494-521	28
α-helix	524-526	3
β-strand	531-533	3	2
α-helix	549-552	4
β-strand	554-559	6	2
β-strand	562-567	6	2
β-strand	591-596	6	2
α-helix	601-608	8
α-helix	613-621	9
β-strand	626-628	3	5
β-strand	632	1	6
β-strand	636-638	3	5
α-helix	640-646	7
α-helix	657-663	7
α-helix	666-686	21
β-strand	687	1	6
α-helix	699-700	2
α-helix	707-714	8
α-helix	716-718	3
β-strand	720-725	6	2
α-helix	728-737	10
β-strand	741-746	6	2
α-helix	748-750	3
α-helix	760-769	10
α-helix	771-775	5
β-strand	779-781	3	2
β-strand	786-790	5	2
α-helix	862-865	4
β-strand	868-877	10	2
β-strand	882	1	1
α-helix	889-892	4
α-helix	894-898	5
β-strand	904-908	5	7
β-strand	916-920	5	7
β-strand	926-931	6	7
β-strand	934-935	2	8
β-strand	938-939	2	8
α-helix	940-956	17
α-helix	965-985	21
β-strand	989-994	6	7
α-helix	1010-1024	15
β-strand	1026	1	9
β-strand	1036	1	10
β-strand	1041	1	10
β-strand	1043	1	9
β-strand	1058	1	7
β-strand	1063-1066	4	7
β-strand	1083	1	11
α-helix	1085-1087	3
α-helix	1091-1099	9
β-strand	1103-1106	4	12
β-strand	1113-1116	4	12
β-strand	1126	1	11
β-strand	1145-1147	3	13
β-strand	1153-1155	3	13
β-strand	1159	1	14
β-strand	1176	1	14
α-helix	1179-1188	10
α-helix	1200-1206	7
α-helix	1209-1222	14
β-strand	1226-1229	4	15
β-strand	1234-1237	4	15
β-strand	1238	1	16
β-strand	1250	1	16
α-helix	1251-1253	3
α-helix	1262-1283	22
α-helix	1295-1306	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cpf1	A	protein	1308	Acidaminococcus sp. (strain BV3L6)	U2UMQ6 (AlphaFold model)
RNA (40-mer)	B	RNA	45	Acidaminococcus sp. BV3L6
DNA (28-mer)	C	DNA	33	Acidaminococcus sp. BV3L6
DNA (8-mer)	D	DNA	8	Acidaminococcus sp. BV3L6

Sequence of entity 1 (A), FASTA

>5KK5_1 CRISPR-associated endonuclease Cpf1 (chains A)
SMTQFEGFTNLYQVSKTLRFELIPQGKTLKHIQEQGFIEEDKARNDHYKELKPIIDRIYK
TYADQCLQLVQLDWENLSAAIDSYRKEKTEETRNALIEEQATYRNAIHDYFIGRTDNLTD
AINKRHAEIYKGLFKAELFNGKVLKQLGTVTTTEHENALLRSFDKFTTYFSGFYENRKNV
FSAEDISTAIPHRIVQDNFPKFKENCHIFTRLITAVPSLREHFENVKKAIGIFVSTSIEE
VFSFPFYNQLLTQTQIDLYNQLLGGISREAGTEKIKGLNEVLNLAIQKNDETAHIIASLP
HRFIPLFKQILSDRNTLSFILEEFKSDEEVIQSFCKYKTLLRNENVLETAEALFNELNSI
DLTHIFISHKKLETISSALCDHWDTLRNALYERRISELTGKITKSAKEKVQRSLKHEDIN
LQEIISAAGKELSEAFKQKTSEILSHAHAALDQPLPTTLKKQEEKEILKSQLDSLLGLYH
LLDWFAVDESNEVDPEFSARLTGIKLEMEPSLSFYNKARNYATKKPYSVEKFKLNFQMPT
LASGWDVNKEKNNGAILFVKNGLYYLGIMPKQKGRYKALSFEPTEKTSEGFDKMYYDYFP
DAAKMIPKCSTQLKAVTAHFQTHTTPILLSNNFIEPLEITKEIYDLNNPEKEPKKFQTAY
AKKTGDQKGYREALCKWIDFTRDFLSKYTKTTSIDLSSLRPSSQYKDLGEYYAELNPLLY
HISFQRIAEKEIMDAVETGKLYLFQIYNKDFAKGHHGKPNLHTLYWTGLFSPENLAKTSI
KLNGQAELFYRPKSRMKRMAHRLGEKMLNKKLKDQKTPIPDTLYQELYDYVNHRLSHDLS
DEARALLPNVITKEVSHEIIKDRRFTSDKFFFHVPITLNYQAANSPSKFNQRVNAYLKEH
PETPIIGIDRGERNLIYITVIDSTGKILEQRSLNTIQQFDYQKKLDNREKERVAARQAWS
VVGTIKDLKQGYLSQVIHEIVDLMIHYQAVVVLANLNFGFKSKRTGIAEKAVYQQFEKML
IDKLNCLVLKDYPAEKVGGVLNPYQLTDQFTSFAKMGTQSGFLFYVPAPYTSKIDPLTGF
VDPFVWKTIKNHESRKHFLEGFDFLHYDVKTGDFILHFKMNRNLSFQRGLPGFMPAWDIV
FEKNETQFDAKGTPFIAGKRIVPVIENHRFTGRYRDLYPANELIALLEEKGIVFRDGSNI
LPKLLENDDSHAIDTMVALIRSVLQMRNSNAATGEDYINSPVRDLNGVCFDSRFQNPEWP
MDADANGAYHIALKGQLLLNHLKESKDLKLQNGISNQDWLAYIQELRN

Sequence of entity 2 (B), FASTA

>5KK5_2 RNA (40-MER) (chains B)
UAAUUUCUACUCUUGUAGAUGAGAAGUCAUUUAAUAAGGCCACUC

Sequence of entity 3 (C), FASTA

>5KK5_3 DNA (28-MER) (chains C)
GAGTGGCCTTATTAAATGACTTCTCGAAACATG

Sequence of entity 4 (D), FASTA

>5KK5_4 DNA (8-mer) (chains D)
CATGTTTC

Primary citation

Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition. Gao, P., Yang, H., Rajashankar, K.R. et al. Cell Res (2016) 26:901-913. DOI 10.1038/cr.2016.88 · PubMed

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
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

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