7VW3: SaCas9-sgRNA-DNA ternary complex

Cryo-EM structure of SaCas9-sgRNA-DNA ternary complex. Determined by electron microscopy at 3.8 Å resolution. Released 15 Mar 2023.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Staphylococcus aureus, synthetic construct
Chains: 4
Atoms: 12,319
Mol. weight: 178.19 kDa
Ligands: MG
Released: 15 Mar 2023

Explore 7VW3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VW3 contains 58 α-helices and 39 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: 58 helices, 39 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	88-94	7
α-helix	102-114	13
β-strand	118	1	2
α-helix	134-145	12
α-helix	150-159	10
α-helix	167-169	3
β-strand	172	1	2
α-helix	173-188	16
α-helix	196-205	10
α-helix	226-229	4
β-strand	236	1	3
β-strand	244	1	3
β-strand	246-247	2	4
α-helix	251-262	12
β-strand	266	1	5
α-helix	277-283	7
α-helix	284-288	5
α-helix	296-298	3
α-helix	300-302	3
β-strand	311	1	5
α-helix	323-325	3
α-helix	327-333	7
α-helix	339-342	4
α-helix	345-357	13
α-helix	363-369	7
α-helix	377-383	7
β-strand	392-393	2	4
α-helix	397-409	13
α-helix	415-420	6
α-helix	439-444	6
α-helix	448-468	21
β-strand	473-477	5	1
α-helix	484-492	9
α-helix	506-509	4
α-helix	511-513	3
α-helix	515-518	4
α-helix	522-529	8
β-strand	533	1	6
β-strand	540	1	6
α-helix	543-548	6
α-helix	550-552	3
β-strand	553-557	5	7
α-helix	561-563	3
β-strand	572-576	5	7
α-helix	577-580	4
α-helix	588-591	4
α-helix	601-611	11
α-helix	617-619	3
α-helix	620-625	6
α-helix	636-640	5
α-helix	651-666	16
β-strand	672-676	5	1
α-helix	678-687	10
α-helix	697-699	3
α-helix	700-714	15
α-helix	722-729	8
α-helix	731-734	4
α-helix	738-740	3
α-helix	747-753	7
α-helix	757-759	3
α-helix	761-764	4
β-strand	770-773	4	1
β-strand	789-793	5	8
β-strand	799-806	8	8
α-helix	817-820	4
α-helix	824-826	3
β-strand	827	1	8
α-helix	828-831	4
α-helix	834-846	13
α-helix	853-861	9
β-strand	866	1	9
α-helix	874-875	2
β-strand	876	1	9
α-helix	877	1
β-strand	879-886	8	8
β-strand	891-892	2	8
β-strand	904-906	3	8
β-strand	911-919	9	10
β-strand	922-929	8	10
β-strand	933-936	4	11
β-strand	939-942	4	11
α-helix	944-952	9
α-helix	960	1
β-strand	961-966	6	10
β-strand	971-974	4	12
β-strand	977-979	3	12
β-strand	980-986	7	13
β-strand	991-995	5	13
α-helix	1001-1008	8
β-strand	1016-1019	4	13
β-strand	1027-1032	6	12
β-strand	1038-1040	3	12
β-strand	1049	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cas9	A	protein	1052	Staphylococcus aureus	J7RUA5 (AlphaFold model)
single-guide RNA	B	RNA	104	synthetic construct
Target DNA strand	C	DNA	40	synthetic construct
Non-target DNA strand	D	DNA	28	synthetic construct

Sequence of entity 1 (A), FASTA

>7VW3_1 CRISPR-associated endonuclease Cas9 (chains A)
KRNYILGLAIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRRSKRGARRLKRRRR
HRIQRVKKLLFDYNLLTDHSELSGINPYEARVKGLSQKLSEEEFSAALLHLAKRRGVHNV
NEVEEDTGNELSTKEQISRNSKALEEKYVAELQLERLKKDGEVRGSINRFKTSDYVKEAK
QLLKVQKAYHQLDQSFIDTYIDLLETRRTYYEGPGEGSPFGWKDIKEWYEMLMGHCTYFP
EELRSVKYAYNADLYNALNDLNNLVITRDENEKLEYYEKFQIIENVFKQKKKPTLKQIAK
EILVNEEDIKGYRVTSTGKPEFTNLKVYHDIKDITARKEIIENAELLDQIAKILTIYQSS
EDIQEELTNLNSELTQEEIEQISNLKGYTGTHNLSLKAINLILDELWHTNDNQIAIFNRL
KLVPKKVDLSQQKEIPTTLVDDFILSPVVKRSFIQSIKVINAIIKKYGLPNDIIIELARE
KNSKDAQKMINEMQKRNRQTNERIEEIIRTTGKENAKYLIEKIKLHDMQEGKCLYSLEAI
PLEDLLNNPFNYEVDHIIPRSVSFDNSFNNKVLVKQEEASKKGNRTPFQYLSSSDSKISY
ETFKKHILNLAKGKGRISKTKKEYLLEERDINRFSVQKDFINRNLVDTRYATRGLMNLLR
SYFRVNNLDVKVKSINGGFTSFLRRKWKFKKERNKGYKHHAEDALIIANADFIFKEWKKL
DKAKKVMENQMFEEKQAESMPEIETEQEYKEIFITPHQIKHIKDFKDYKYSHRVDKKPNR
ELINDTLYSTRKDDKGNTLIVNNLNGLYDKDNDKLKKLINKSPEKLLMYHHDPQTYQKLK
LIMEQYGDEKNPLYKYYEETGNYLTKYSKKDNGPVIKKIKYYGNKLNAHLDITDDYPNSR
NKVVKLSLKPYRFDVYLDNGVYKFVTVKNLDVIKKENYYEVNSKCYEEAKKLKKISNQAE
FIASFYNNDLIKINGELYRVIGVNNDLLNRIEVNMIDITYREYLENMNDKRPPRIIKTIA
SKTQSIKKYSTDILGNLYEVKSKKHPQIIKKG

Sequence of entity 2 (B), FASTA

>7VW3_2 single-guide RNA (chains B)
GUACCGCUCCAGUCGUUCAUGGUUUUAGUACUCUGGAAACAGAAUCUACUAAAACAAGGC
AAAAUGCCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUUUUUUU

Sequence of entity 3 (C), FASTA

>7VW3_3 Target DNA strand (chains C)
AGAGTACTAAAACATTCAACATGAACGACTGGAGCGGTAC

Sequence of entity 4 (D), FASTA

>7VW3_4 Non-target DNA strand (chains D)
TCGTTCATGTTGAATGTTTTAGTACTCT

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3

Primary citation

Full-Length Model of SaCas9-sgRNA-DNA Complex in Cleavage State. Du, W., Zhu, H., Qian, J. et al. Int J Mol Sci (2023) 24. DOI 10.3390/ijms24021204 · 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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