8ZCY: CRISPR-associated endonuclease Cas9

Cryo-EM structure of eSaCas9_NNG-guide RNA-target DNA complex in an interrogation state. Determined by electron microscopy at 3.17 Å resolution. Released 5 Nov 2025.

Method: Electron microscopy
Resolution: 3.17 Å
Organism: Staphylococcus aureus
Chains: 4
Atoms: 8,307
Mol. weight: 182.9 kDa
Released: 5 Nov 2025

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

Secondary structure: helices and β-sheets

8ZCY contains 31 α-helices and 33 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: 31 helices, 33 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	439-443	5
α-helix	448-468	21
β-strand	473-478	6	1
α-helix	484-511	28
α-helix	516-519	4
α-helix	521-530	10
β-strand	533-534	2	2
β-strand	539-540	2	2
α-helix	543-548	6
β-strand	553-557	5	3
α-helix	561-564	4
α-helix	569-571	3
β-strand	572-576	5	3
α-helix	577-583	7
α-helix	588-592	5
α-helix	601-612	12
α-helix	620-626	7
α-helix	635-645	11
α-helix	651-667	17
β-strand	672-675	4	1
α-helix	678-687	10
α-helix	699-717	19
α-helix	719-721	3
α-helix	722-728	7
α-helix	747-753	7
α-helix	759-765	7
β-strand	770-773	4	1
β-strand	776	1	4
β-strand	789-790	2	5
β-strand	791-793	3	6
β-strand	799-805	7	6
α-helix	815-822	8
α-helix	824-826	3
β-strand	827	1	6
α-helix	828-832	5
α-helix	834-846	13
α-helix	853-861	9
β-strand	866	1	7
α-helix	874-875	2
β-strand	876	1	7
α-helix	877	1
β-strand	880-886	7	6
α-helix	887	1
β-strand	891-892	2	5
α-helix	894-896	3
β-strand	904-906	3	5
β-strand	911-919	9	8
β-strand	922-929	8	8
β-strand	933-935	3	9
β-strand	940-942	3	9
α-helix	944-953	10
β-strand	961-966	6	8
β-strand	968	1	4
β-strand	971-974	4	10
β-strand	977-986	10	10
β-strand	991-995	5	10
α-helix	1001-1008	8
β-strand	1016-1019	4	10
β-strand	1027-1032	6	10
β-strand	1038-1041	4	10
β-strand	1050-1051	2	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cas9	A	protein	1056	Staphylococcus aureus	J7RUA5 (AlphaFold model)
sgRNA	B	RNA	99	Staphylococcus aureus
Non-target DNA strand	C	DNA	43	Staphylococcus aureus
Target DNA strand	D	DNA	43	Staphylococcus aureus

Sequence of entity 1 (A), FASTA

>8ZCY_1 CRISPR-associated endonuclease Cas9 (chains A)
GSHMKRNYILGLDIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRRSKRGARRLK
RRRRHRIQRVKKLLFDYNLLTDHSELSGINPYEARVKGLSQKLSEEEFSAALLHLAKRRG
VHNVNEVEEDTGNELSTKEQISRNSKALEEKYVAELQLERLKKDGEVRGSINRFKTSDYV
KEAKQLLKVQKAYHQLDQSFIDTYIDLLETRRTYYEGPGEGSPFGWKDIKEWYEMLMGHC
TYFPEELRSVKYAYNADLYNALNDLNNLVITRDENEKLEYYEKFQIIENVFKQKKKPTLK
QIAKEILVNEEDIKGYRVTSTGKPEFTNLKVYHDIKDITARKEIIENAELLDQIAKILTI
YQSSEDIQEELTNLNSELTQEEIEQISNLKGYTGTHNLSLKAINLILDELWHTNDAQIAI
FNALKLVPKKVDLSQQKEIPTTLVDDFILSPVVKRSFIQSIKVINAIIKKYGLPNDIIIE
LAREKNSKDAQKMINEMQKRNRQTNERIEEIIRTTGKENAKYLIEKIKLHDMQEGKCLYS
LEAIPLEDLLNNPFNYEVDHIIPRSVSFDNSFNNKVLVKQEENSKKGNRTPFQYLSSSDS
KISYETFKKHILNLAKGKGRISKTKKEYLLEERDINRFSVQKDFINRNLVDTRYATRGLM
NLLRSYFRVNNLDVKVKSINGGFTSFLRRKWKFKKERNKGYKHHAEDALIIANADFIFKE
WKKLDKAKKVMENQMFEEKQAESMPEIETEQEYKEIFITPHQIKHIKDFKDYKYSHRVDK
KPNRKLINDTLYSTRKDDKGNTRIVNNLNGLYDKDNDKLKKLINKSPEKLLMYHHDPQTY
QKLKLIMEQYGDEKNPLYKYYEETGNYLTKYSKKDNGPVIKKIKYYGNKLNAHLDITDDY
PNSRNKVVKLSLKPYRFDVYLDNGVYKFVKVNNLDVIKKENYYEVNSKCYEEAKKLKKIS
NQAEFIASFYRNDLIKINGELYRVIGVASDLLNAIEVNMIDITYREYLENMNDKRPPRIF
KTISSKTQSIKKYSTDILGNLYEVKSKKHPQIIKKG

Sequence of entity 2 (B), FASTA

>8ZCY_2 sgRNA (chains B)
GGGAAAUUAGGUGCGCUUGGCGUUUUAGUACUCUGGAAACAGAAUCUACUAAAACAAGGC
AAAAUGCCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUA

Sequence of entity 3 (C), FASTA

>8ZCY_3 Non-target DNA strand (chains C)
ATTTGAATAGGCAAGCCAAGCGCACCTAATTTCCCGTATTTAG

Sequence of entity 4 (D), FASTA

>8ZCY_4 Target DNA strand (chains D)
CTAAATACGGGAAATTAGGTGCGCTTGGCTTGCCTATTCAAAT

Primary citation

Engineering a compact high-fidelity Staphylococcus aureus Cas9 variant with broader targeting range and mechanistic insights into its activation. Omura, S.N., Nakagawa, R., Kajimoto, S. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-71626-2 · 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…
8JFT 3.31 Å, Cryo-EM structure of SaCas9-AcrIIA15 CTD-sgRNA complex

Browse structure collections

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