8Y0D: SauCas9

Crystal structure of SauCas9 in complex with sgRNA and 20nt ssDNA target. Determined by X-ray diffraction at 3.92 Å resolution. Released 1 Jan 2025.

Method: X-ray diffraction
Resolution: 3.92 Å
Organism: Staphylococcus aureus
Chains: 3
Atoms: 10,023
Mol. weight: 153.89 kDa
Released: 1 Jan 2025

Explore 8Y0D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y0D contains 52 α-helices and 42 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: 52 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	1
β-strand	15-22	8	1
β-strand	28-35	8	1
α-helix	37-39	3
α-helix	46-74	29
α-helix	88-97	10
α-helix	104-114	11
β-strand	118	1	2
α-helix	134-145	12
α-helix	150-160	11
α-helix	167-169	3
β-strand	172	1	2
α-helix	173-187	15
α-helix	197-206	10
α-helix	227-230	4
β-strand	245-247	3	3
α-helix	251-263	13
β-strand	266	1	4
α-helix	277-282	6
α-helix	283-288	6
α-helix	296-302	7
β-strand	311	1	4
β-strand	315	1	5
β-strand	321	1	5
α-helix	327-333	7
α-helix	339-342	4
α-helix	345-357	13
α-helix	361-369	9
α-helix	377-383	7
β-strand	392-396	5	3
α-helix	397-399	3
α-helix	405-408	4
α-helix	414-420	7
α-helix	439-441	3
α-helix	448-468	21
β-strand	473-478	6	1
α-helix	502-511	10
α-helix	521-530	10
β-strand	533	1	6
β-strand	540	1	6
α-helix	543-548	6
β-strand	553-557	5	7
α-helix	569-571	3
β-strand	572-576	5	7
α-helix	577-583	7
α-helix	588-593	6
α-helix	601-612	12
α-helix	617-619	3
α-helix	620-626	7
α-helix	635-641	7
α-helix	642-646	5
α-helix	653-666	14
β-strand	672-675	4	1
α-helix	680-687	8
α-helix	698-700	3
α-helix	702-717	16
α-helix	747-753	7
α-helix	761-765	5
β-strand	770-773	4	1
β-strand	789	1	8
β-strand	790-793	4	9
β-strand	799-805	7	9
α-helix	815-820	6
α-helix	824-826	3
β-strand	827	1	9
α-helix	828-831	4
α-helix	834-846	13
α-helix	853-861	9
β-strand	866	1	10
α-helix	867-868	2
α-helix	874-875	2
β-strand	876	1	10
α-helix	877	1
β-strand	880-883	4	9
β-strand	891-892	2	8
α-helix	894-896	3
β-strand	905-906	2	8
β-strand	911-913	3	11
β-strand	915-919	5	12
β-strand	922-925	4	12
β-strand	928-929	2	11
β-strand	934-935	2	13
β-strand	940-941	2	13
α-helix	944-953	10
β-strand	961-965	5	12
β-strand	971-974	4	14
β-strand	977-986	10	14
β-strand	991-995	5	14
α-helix	1001-1008	8
β-strand	1016	1	14
β-strand	1019	1	14
β-strand	1027-1032	6	14
β-strand	1038-1040	3	14
β-strand	1049-1050	2	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA (73-mer)	B	RNA	74	Staphylococcus aureus
DNA (5'-d(pgptpapapapgptptpapapaptpapgpcpapgpap*c)-3')	C	DNA	20	Staphylococcus aureus
CRISPR-associated endonuclease Cas9	A	protein	1053	Staphylococcus aureus	J7RUA5 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8Y0D_1 RNA (73-MER) (chains B)
GGUCUGCUAUUUAACUUUACGUUUUAGUACUCUGGAAACAGAAUCUACUAAAACAAGGCA
AAAUGCCGUGUUUC

Sequence of entity 2 (C), FASTA

>8Y0D_2 DNA (5'-D(P*GP*TP*AP*AP*AP*GP*TP*TP*AP*AP*AP*TP*AP*GP*CP*AP*GP*AP*C)-3') (chains C)
GTAAAGTTAAATAGCAGACC

Sequence of entity 3 (A), FASTA

>8Y0D_3 CRISPR-associated endonuclease Cas9 (chains A)
MKRNYILGLDIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRRSKRGARRLKRRR
RHRIQRVKKLLFDYNLLTDHSELSGINPYEARVKGLSQKLSEEEFSAALLHLAKRRGVHN
VNEVEEDTGNELSTKEQISRNSKALEEKYVAELQLERLKKDGEVRGSINRFKTSDYVKEA
KQLLKVQKAYHQLDQSFIDTYIDLLETRRTYYEGPGEGSPFGWKDIKEWYEMLMGHCTYF
PEELRSVKYAYNADLYNALNDLNNLVITRDENEKLEYYEKFQIIENVFKQKKKPTLKQIA
KEILVNEEDIKGYRVTSTGKPEFTNLKVYHDIKDITARKEIIENAELLDQIAKILTIYQS
SEDIQEELTNLNSELTQEEIEQISNLKGYTGTHNLSLKAINLILDELWHTNDNQIAIFNR
LKLVPKKVDLSQQKEIPTTLVDDFILSPVVKRSFIQSIKVINAIIKKYGLPNDIIIELAR
EKNSKDAQKMINEMQKRNRQTNERIEEIIRTTGKENAKYLIEKIKLHDMQEGKCLYSLEA
IPLEDLLNNPFNYEVDHIIPRSVSFDNSFNNKVLVKQEEASKKGNRTPFQYLSSSDSKIS
YETFKKHILNLAKGKGRISKTKKEYLLEERDINRFSVQKDFINRNLVDTRYATRGLMNLL
RSYFRVNNLDVKVKSINGGFTSFLRRKWKFKKERNKGYKHHAEDALIIANADFIFKEWKK
LDKAKKVMENQMFEEKQAESMPEIETEQEYKEIFITPHQIKHIKDFKDYKYSHRVDKKPN
RELINDTLYSTRKDDKGNTLIVNNLNGLYDKDNDKLKKLINKSPEKLLMYHHDPQTYQKL
KLIMEQYGDEKNPLYKYYEETGNYLTKYSKKDNGPVIKKIKYYGNKLNAHLDITDDYPNS
RNKVVKLSLKPYRFDVYLDNGVYKFVTVKNLDVIKKENYYEVNSKAYEEAKKLKKISNQA
EFIASFYNNDLIKINGELYRVIGVNNDLLNRIEVNMIDITYREYLENMNDKRPPRIIKTI
ASKTQSIKKYSTDILGNLYEVKSKKHPQIIKKG

Primary citation

DNA target binding-induced pre-crRNA processing in type II and V CRISPR-Cas systems. Chen, J., Lin, X., Xiang, W. et al. Nucleic Acids Res (2025) 53. DOI 10.1093/nar/gkae1241 · PubMed

Other PDB entries of the same protein (UniProt J7RUA5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7ENH 2.1 Å, Crystal structure of cas and anti-cas protein complex
7EL1 2.22 Å, Structure of a protein from bacteria
5CZZ 2.6 Å, Crystal structure of Staphylococcus aureus Cas9 in complex with sgRNA and target DNA…
7ENI 2.63 Å, Crystal structure of cas and anti-cas protein complex
5AXW 2.7 Å, Crystal structure of Staphylococcus aureus Cas9 in complex with sgRNA and target DNA…
8ZD0 2.76 Å, Cryo-EM structure of eSaCas9_NNG-guide RNA-target DNA complex in a translocation state
9MB7 2.88 Å, Cryo-EM structure of eSaCas9-NNG-guide RNA-mismatched target DNA complex
8ZCZ 2.9 Å, Cryo-EM structure of eSaCas9_NNG-guide RNA-target DNA complex in an intermediate state
8YWH 2.97 Å, Cryo-EM structure of small and dead form SaCas9-RNA-DNA ternary complex (sdCas9)
9MB6 3.01 Å, Cryo-EM structure of wild-type SaCas9-guide RNA-mismatched target DNA complex
8ZDA 3.14 Å, Cryo-EM structure of eSaCas9_NNG-guide RNA-target DNA complex in a catalytically active…
8ZCY 3.17 Å, Cryo-EM structure of eSaCas9_NNG-guide RNA-target DNA complex in an interrogation state

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