8YWH: SCas9

Cryo-EM structure of small and dead form SaCas9-RNA-DNA ternary complex (sdCas9). Determined by electron microscopy at 2.97 Å resolution. Released 2 Apr 2025.

Method: Electron microscopy
Resolution: 2.97 Å
Organisms: Staphylococcus aureus, synthetic construct
Chains: 4
Atoms: 9,957
Mol. weight: 172.05 kDa
Released: 2 Apr 2025

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

Secondary structure: helices and β-sheets

8YWH contains 41 α-helices and 36 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: 41 helices, 36 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	41-73	33
α-helix	88-95	8
α-helix	102-114	13
β-strand	118	1	2
α-helix	120-123	4
α-helix	134-143	10
α-helix	150-160	11
α-helix	167-169	3
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
β-strand	245-247	3	4
α-helix	251-264	14
β-strand	266	1	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	311	1	5
α-helix	327-335	9
α-helix	339-343	5
α-helix	345-357	13
α-helix	361-371	11
α-helix	377-385	9
β-strand	392-396	5	4
α-helix	397-407	11
α-helix	414-420	7
α-helix	436-437	2
α-helix	439-443	5
α-helix	448-467	20
β-strand	473-478	6	1
α-helix	482-499	18
β-strand	505-507	3	1
α-helix	511-519	9
α-helix	532-548	17
β-strand	603-606	4	1
β-strand	609	1	6
β-strand	621-626	6	7
β-strand	632-638	7	7
α-helix	648-655	8
α-helix	657-659	3
β-strand	660	1	7
α-helix	661-664	4
α-helix	667-680	14
α-helix	686-694	9
β-strand	699	1	8
α-helix	707-708	2
β-strand	709	1	8
α-helix	710	1
β-strand	713-719	7	7
β-strand	723-725	3	7
α-helix	727-729	3
β-strand	737-740	4	7
α-helix	742-743	2
β-strand	744-752	9	9
β-strand	755-762	8	9
β-strand	766-769	4	10
β-strand	772-775	4	10
α-helix	777-787	11
β-strand	795-799	5	9
β-strand	801	1	6
β-strand	804-807	4	11
β-strand	810-819	10	11
β-strand	824-828	5	11
α-helix	834-841	8
β-strand	849-852	4	11
β-strand	860-865	6	11
β-strand	871-873	3	11
β-strand	882-884	3	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
sCas9 (Compact SaCas9)	A	protein	886	Staphylococcus aureus	J7RUA5 (AlphaFold model)
sgRNA	B	RNA	98	synthetic construct
Target DNA	C	DNA	59	synthetic construct
Non-target DNA	D	DNA	59	synthetic construct

Sequence of entity 1 (A), FASTA

>8YWH_1 sCas9 (Compact SaCas9) (chains A)
MKRNYILGLAIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRRSKRGARRLKRRR
RHRIQRVKKLLFDYNLLTDHSELSGINPYEARVKGLSQKLSEEEFSAALLHLAKRRGVHN
VNEVEEDTGNELSTKEQISRNSKALEEKYVAELQLERLKKDGEVRGSINRFKTSDYVKEA
KQLLKVQKAYHQLDQSFIDTYIDLLETRRTYYEGPGEGSPFGWKDIKEWYEMLMGHCTYF
PEELRSVKYAYNADLYNALNDLNNLVITRDENEKLEYYEKFQIIENVFKQKKKPTLKQIA
KEILVNEEDIKGYRVTSTGKPEFTNLKVYHDIKDITARKEIIENAELLDQIAKILTIYQS
SEDIQEELTNLNSELTQEEIEQISNLKGYTGTHNLSLKAINLILDELWHTNDNQIAIFNR
LKLVPKKVDLSQQKEIPTTLVDDFILSPVVKRSFIQSIKVINAIIKKYGLPNDIIIELAR
GGSYATRGLMNLLRSYFRVNNLDVKVKSINGGFTSFLRRKWKFKKERNKGYKHHAEDALI
IANADFIFKEWKKLDKAKKVMENQMFEEKQAESMPEIETEQEYKEIFITPHQIKHIKDFK
DYKYSHRVDKKPNRELINDTLYSTRKDDKGNTLIVNNLNGLYDKDNDKLKKLINKSPEKL
LMYHHDPQTYQKLKLIMEQYGDEKNPLYKYYEETGNYLTKYSKKDNGPVIKKIKYYGNKL
NAHLDITDDYPNSRNKVVKLSLKPYRFDVYLDNGVYKFVTVKNLDVIKKENYYEVNSKCY
EEAKKLKKISNQAEFIASFYNNDLIKINGELYRVIGVNNDLLNRIEVNMIDITYREYLEN
MNDKRPPRIIKTIASKTQSIKKYSTDILGNLYEVKSKKHPQIIKKG

Sequence of entity 2 (B), FASTA

>8YWH_2 sgRNA (chains B)
GAUCUGAGUCCGGUAGCGCUAGUUUUAGUACUCUGGAAACAGAAUCUACUAAAACAAGGC
AAAAUGCCGUGUUUAUCUCGUCAACUUGUUGGCGAGAU

Sequence of entity 3 (C), FASTA

>8YWH_3 Target DNA (chains C)
GAACCGTCAGATCCGCTAGCGCTACCGGACTCAGATCTCGAGTTCAAGCTTCGAATTCT

Sequence of entity 4 (D), FASTA

>8YWH_4 Non-target DNA (chains D)
AGAATTCGAAGCTTGAACTCGAGATCTGAGTCCGGTAGCGCTAGCGGATCTGACGGTTC

Primary citation

Structure-Guided Engineering of Thermodynamically Enhanced SaCas9 for Improved Gene Suppression. Kang, E.S., Kim, N.H., Lim, H.K. et al. Adv Mater (2025) 37:e2404680-e2404680. DOI 10.1002/adma.202404680 · 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
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

Browse structure collections

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