8JG9: SaCas9-sgRNA-AcrIIA15-promoter DNA dimer

Cryo-EM structure of the SaCas9-sgRNA-AcrIIA15-promoter DNA dimer. Determined by electron microscopy at 3.82 Å resolution. Released 28 Feb 2024.

Method: Electron microscopy
Resolution: 3.82 Å
Organisms: Staphylococcus aureus, Staphylococcus delphini
Chains: 8
Atoms: 24,264
Mol. weight: 366.6 kDa
Released: 28 Feb 2024

Explore 8JG9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JG9 contains 137 α-helices and 98 β-strands across 4 chains. 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: 56 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	1
β-strand	15-22	8	1
β-strand	31-35	5	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	121-123	3
α-helix	134-144	11
α-helix	150-160	11
β-strand	172	1	2
α-helix	173-187	15
α-helix	195-206	12
α-helix	226-234	9
β-strand	236	1	3
β-strand	244	1	3
α-helix	245	1
β-strand	246	1	4
α-helix	247	1
α-helix	251-264	14
β-strand	266-267	2	5
α-helix	277-290	14
α-helix	296-303	8
α-helix	307-309	3
β-strand	310-311	2	5
β-strand	315	1	6
β-strand	321	1	6
α-helix	327-335	9
α-helix	339-342	4
α-helix	345-357	13
α-helix	361-370	10
α-helix	377-383	7
β-strand	394	1	4
α-helix	397-409	13
α-helix	414-421	8
α-helix	439-443	5
α-helix	448-468	21
β-strand	473-478	6	1
α-helix	484-512	29
α-helix	516-519	4
α-helix	521-529	9
β-strand	533	1	7
β-strand	540	1	7
α-helix	543-548	6
α-helix	550-552	3
β-strand	553-557	5	8
α-helix	561-564	4
α-helix	569-571	3
β-strand	572-576	5	8
α-helix	577-583	7
α-helix	588-593	6
α-helix	601-613	13
α-helix	614-616	3
α-helix	620-626	7
α-helix	635-645	11
α-helix	651-666	16
β-strand	672-675	4	1
α-helix	678-687	10
α-helix	699-713	15
α-helix	719-721	3
α-helix	722-729	8
α-helix	747-754	8
α-helix	761-765	5
β-strand	770-772	3	1
β-strand	784	1	9
β-strand	790	1	10
β-strand	791-793	3	11
β-strand	799-801	3	11
β-strand	803-805	3	12
α-helix	815-822	8
α-helix	824-826	3
β-strand	827	1	12
α-helix	829-832	4
α-helix	834-846	13
α-helix	853-861	9
α-helix	866-868	3
α-helix	874-876	3
β-strand	880-882	3	12
β-strand	886	1	11
β-strand	891-892	2	13
β-strand	904	1	10
β-strand	905-906	2	13
β-strand	909	1	9
β-strand	911-919	9	14
β-strand	922-929	8	14
α-helix	930-932	3
β-strand	933-936	4	15
β-strand	939-942	4	15
α-helix	944-953	10
α-helix	960	1
β-strand	961-966	6	14
β-strand	971-974	4	16
β-strand	977-986	10	16
β-strand	991-995	5	16
α-helix	1001-1006	6
β-strand	1017-1019	3	16
β-strand	1027-1032	6	16
β-strand	1038-1040	3	16
β-strand	1050-1051	2	15

Chain C: 13 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	2-9	8
α-helix	15-22	8
α-helix	26-34	9
α-helix	39-41	3
β-strand	43	1	33
α-helix	44-58	15
β-strand	62-69	8	35
β-strand	76-81	6	35
α-helix	84-94	11
α-helix	97-99	3
α-helix	101	1
α-helix	104-113	10
α-helix	117-120	4
β-strand	123	1	11
α-helix	130-138	9
α-helix	141-144	4
α-helix	149-154	6
β-strand	162-169	8	35

Chain D: 56 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	17
β-strand	15-22	8	17
β-strand	31-35	5	17
α-helix	37-39	3
α-helix	41-73	33
α-helix	88-95	8
α-helix	102-114	13
β-strand	118	1	18
α-helix	121-123	3
α-helix	134-144	11
α-helix	150-160	11
β-strand	172	1	18
α-helix	173-187	15
α-helix	195-206	12
α-helix	226-234	9
β-strand	236	1	19
β-strand	244	1	19
α-helix	245	1
β-strand	246	1	20
α-helix	247	1
α-helix	251-264	14
β-strand	266-267	2	21
α-helix	277-290	14
α-helix	296-303	8
α-helix	307-309	3
β-strand	310-311	2	21
β-strand	315	1	22
β-strand	321	1	22
α-helix	327-335	9
α-helix	339-342	4
α-helix	345-357	13
α-helix	361-370	10
α-helix	377-383	7
β-strand	394	1	20
α-helix	397-409	13
α-helix	414-421	8
α-helix	439-443	5
α-helix	448-468	21
β-strand	473-478	6	17
α-helix	484-512	29
α-helix	516-519	4
α-helix	521-529	9
β-strand	533	1	23
β-strand	540	1	23
α-helix	543-548	6
α-helix	550-552	3
β-strand	553-557	5	24
α-helix	561-564	4
α-helix	569-571	3
β-strand	572-576	5	24
α-helix	577-583	7
α-helix	588-593	6
α-helix	601-613	13
α-helix	614-616	3
α-helix	620-626	7
α-helix	635-645	11
α-helix	651-666	16
β-strand	672-675	4	17
α-helix	678-687	10
α-helix	699-713	15
α-helix	719-721	3
α-helix	722-728	7
α-helix	747-754	8
α-helix	761-765	5
β-strand	770-772	3	17
β-strand	784	1	25
β-strand	790	1	26
β-strand	791-793	3	27
β-strand	799-801	3	27
β-strand	803-805	3	28
α-helix	815-822	8
α-helix	824-826	3
β-strand	827	1	28
α-helix	829-832	4
α-helix	834-846	13
α-helix	853-861	9
α-helix	866-868	3
α-helix	874-876	3
β-strand	880-882	3	28
β-strand	886	1	27
β-strand	891-892	2	29
β-strand	904	1	26
β-strand	905-906	2	29
β-strand	909	1	25
β-strand	911-919	9	30
β-strand	922-929	8	30
α-helix	930-932	3
β-strand	933-936	4	31
β-strand	939-942	4	31
α-helix	944-953	10
α-helix	960	1
β-strand	961-966	6	30
β-strand	971-974	4	32
β-strand	977-986	10	32
β-strand	991-995	5	32
α-helix	1001-1006	6
β-strand	1017-1019	3	32
β-strand	1027-1032	6	32
β-strand	1038-1040	3	32
β-strand	1050-1051	2	31

Chain F: 12 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	2-9	8
α-helix	15-22	8
α-helix	26-34	9
α-helix	39-41	3
β-strand	43	1	33
α-helix	44-56	13
β-strand	62-69	8	34
β-strand	76-81	6	34
α-helix	84-94	11
α-helix	101	1
α-helix	104-113	10
α-helix	117-120	4
β-strand	123	1	27
α-helix	130-138	9
α-helix	141-144	4
α-helix	149-154	6
β-strand	162-169	8	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cas9	A, D	protein	1053	Staphylococcus aureus	J7RUA5 (AlphaFold model)
sgRNA	B, E	RNA	98	Staphylococcus aureus
AcrIIA15	C, F	protein	171	Staphylococcus delphini
DNA (25-mer)	G	DNA	25	Staphylococcus delphini
DNA (25-mer)	H	DNA	25	Staphylococcus delphini

Sequence of entity 1 (A, D), FASTA

>8JG9_1 CRISPR-associated endonuclease Cas9 (chains A, D)
MKRNYILGLDIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRRSKRGARRLKRRR
RHRIQRVKKLLFDYNLLTDHSELSGINPYEARVKGLSQKLSEEEFSAALLHLAKRRGVHN
VNEVEEDTGNELSTKEQISRNSKALEEKYVAELQLERLKKDGEVRGSINRFKTSDYVKEA
KQLLKVQKAYHQLDQSFIDTYIDLLETRRTYYEGPGEGSPFGWKDIKEWYEMLMGHCTYF
PEELRSVKYAYNADLYNALNDLNNLVITRDENEKLEYYEKFQIIENVFKQKKKPTLKQIA
KEILVNEEDIKGYRVTSTGKPEFTNLKVYHDIKDITARKEIIENAELLDQIAKILTIYQS
SEDIQEELTNLNSELTQEEIEQISNLKGYTGTHNLSLKAINLILDELWHTNDNQIAIFNR
LKLVPKKVDLSQQKEIPTTLVDDFILSPVVKRSFIQSIKVINAIIKKYGLPNDIIIELAR
EKNSKDAQKMINEMQKRNRQTNERIEEIIRTTGKENAKYLIEKIKLHDMQEGKCLYSLEA
IPLEDLLNNPFNYEVDHIIPRSVSFDNSFNNKVLVKQEENSKKGNRTPFQYLSSSDSKIS
YETFKKHILNLAKGKGRISKTKKEYLLEERDINRFSVQKDFINRNLVDTRYATRGLMNLL
RSYFRVNNLDVKVKSINGGFTSFLRRKWKFKKERNKGYKHHAEDALIIANADFIFKEWKK
LDKAKKVMENQMFEEKQAESMPEIETEQEYKEIFITPHQIKHIKDFKDYKYSHRVDKKPN
RELINDTLYSTRKDDKGNTLIVNNLNGLYDKDNDKLKKLINKSPEKLLMYHHDPQTYQKL
KLIMEQYGDEKNPLYKYYEETGNYLTKYSKKDNGPVIKKIKYYGNKLNAHLDITDDYPNS
RNKVVKLSLKPYRFDVYLDNGVYKFVTVKNLDVIKKENYYEVNSKCYEEAKKLKKISNQA
EFIASFYNNDLIKINGELYRVIGVNNDLLNRIEVNMIDITYREYLENMNDKRPPRIIKTI
ASKTQSIKKYSTDILGNLYEVKSKKHPQIIKKG

Sequence of entity 2 (B, E), FASTA

>8JG9_2 sgRNA (chains B, E)
GGUCUGCUAUUUCUAUUUACGUUUUAGUACUCUGGAAACAGAAUCUACUAAAACAAGGCA
AAAUGCCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUC

Sequence of entity 3 (C, F), FASTA

>8JG9_3 AcrIIA15 (chains C, F)
SMRKTIERLLNSELSSNSIAVRTGVSQAVISKLRNGKKELGNLTLNSAEKLFEYQKEMEK
VDTWIVYRGRTADMNKSYIAEGSTYEEVYNNFVDKYGYDVLDEDIYEIQLLKKNGENLDD
YDVDSDGINNYDKLDEFRESDYVDLEDYDYRELFENSSSQVYYHEFEITHE

Sequence of entity 4 (G), FASTA

>8JG9_4 DNA (25-MER) (chains G)
ATAATTATGACAAATGTCATAGAAA

Sequence of entity 5 (H), FASTA

>8JG9_5 DNA (25-MER) (chains H)
TTTTCTATGACATTTGTCATAATTA

Primary citation

An anti-CRISPR that represses its own transcription while blocking Cas9-target DNA binding. Deng, X., Sun, W., Li, X. et al. Nat Commun (2024) 15:1806-1806. DOI 10.1038/s41467-024-45987-5 · 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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