8ZD0: CRISPR-associated endonuclease Cas9

Cryo-EM structure of eSaCas9_NNG-guide RNA-target DNA complex in a translocation state. Determined by electron microscopy at 2.76 Å resolution. Released 5 Nov 2025.

Method: Electron microscopy
Resolution: 2.76 Å
Organism: Staphylococcus aureus
Chains: 4
Atoms: 10,185
Mol. weight: 182.92 kDa
Ligands: MG
Released: 5 Nov 2025

Explore 8ZD0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ZD0 contains 44 α-helices and 40 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: 44 helices, 40 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	41-73	33
α-helix	88-95	8
α-helix	99-101	3
α-helix	102-114	13
β-strand	118	1	2
α-helix	134-144	11
α-helix	150-160	11
β-strand	172	1	2
α-helix	173-190	18
α-helix	195-206	12
α-helix	226-233	8
β-strand	236	1	3
β-strand	244	1	3
α-helix	245-246	2
β-strand	247	1	4
α-helix	251-264	14
β-strand	266-267	2	5
α-helix	275-276	2
α-helix	277-283	7
α-helix	284-288	5
α-helix	296-303	8
α-helix	307-309	3
β-strand	310-311	2	5
β-strand	314-315	2	6
β-strand	321-322	2	6
α-helix	327-335	9
α-helix	339-342	4
α-helix	345-357	13
α-helix	361-369	9
α-helix	377-383	7
β-strand	392	1	4
α-helix	397-409	13
α-helix	414-420	7
α-helix	439-443	5
α-helix	448-468	21
β-strand	473-474	2	1
β-strand	477	1	1
α-helix	651-667	17
β-strand	672-673	2	1
α-helix	678-687	10
α-helix	694-696	3
α-helix	699-714	16
α-helix	757-765	9
β-strand	770-773	4	1
α-helix	774-775	2
β-strand	776	1	7
β-strand	789-790	2	8
β-strand	791-793	3	9
β-strand	799-805	7	9
α-helix	815-822	8
α-helix	824-826	3
β-strand	827	1	9
α-helix	828-832	5
α-helix	834-846	13
α-helix	853-861	9
β-strand	866	1	10
α-helix	874-875	2
β-strand	876	1	10
α-helix	877	1
β-strand	880-886	7	9
α-helix	887	1
β-strand	891-892	2	8
α-helix	894-896	3
β-strand	904-906	3	8
α-helix	909-910	2
β-strand	911-919	9	11
β-strand	922-929	8	11
α-helix	930-932	3
β-strand	933-935	3	12
β-strand	940-942	3	12
α-helix	944-953	10
β-strand	961-966	6	11
β-strand	968	1	7
β-strand	971-974	4	13
β-strand	977-986	10	13
β-strand	991-995	5	13
α-helix	1001-1008	8
β-strand	1016-1019	4	13
β-strand	1027-1032	6	13
β-strand	1038-1040	3	13
β-strand	1050-1051	2	12

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
Target DNA strand	C	DNA	43	Staphylococcus aureus
Non-target DNA strand	D	DNA	43	Staphylococcus aureus

Sequence of entity 1 (A), FASTA

>8ZD0_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

>8ZD0_2 sgRNA (chains B)
GGGAAAUUAGGUGCGCUUGGCGUUUUAGUACUCUGGAAACAGAAUCUACUAAAACAAGGC
AAAAUGCCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUA

Sequence of entity 3 (C), FASTA

>8ZD0_3 Target DNA strand (chains C)
ATTTGAATAGGCAAGCCAAGCGCACCTAATTTCCCGTATTTAG

Sequence of entity 4 (D), FASTA

>8ZD0_4 Non-target DNA strand (chains D)
CTAAATACGGGAAATTAGGTGCGCTTGGCTTGCCTATTCAAAT

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

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…
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
8JFT 3.31 Å, Cryo-EM structure of SaCas9-AcrIIA15 CTD-sgRNA complex

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