6O0Y: CRISPR-associated endonuclease Cas9/Csn1

Conformational states of Cas9-sgRNA-DNA ternary complex in the presence of magnesium. Determined by electron microscopy at 3.37 Å resolution. Released 10 Jul 2019.

Method: Electron microscopy
Resolution: 3.37 Å
Organisms: Streptococcus pyogenes, synthetic construct
Chains: 5
Atoms: 11,828
Mol. weight: 216.63 kDa
Released: 10 Jul 2019

Explore 6O0Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6O0Y contains 66 α-helices and 47 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: 66 helices, 47 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	1
β-strand	15-21	7	1
β-strand	29-33	5	2
β-strand	35-36	2	3
β-strand	42-46	5	2
β-strand	48-52	5	1
α-helix	54-56	3
α-helix	60-91	32
α-helix	97-102	6
β-strand	116	1	4
β-strand	120	1	4
α-helix	122-131	10
α-helix	136-144	9
α-helix	151-163	13
β-strand	167	1	5
α-helix	316-342	27
α-helix	344-346	3
α-helix	347-351	5
α-helix	359-363	5
α-helix	369-382	14
α-helix	387-393	7
α-helix	405-409	5
β-strand	411	1	5
α-helix	412-426	15
α-helix	431-435	5
α-helix	437-445	9
β-strand	467	1	6
β-strand	482	1	6
α-helix	484-493	10
β-strand	498	1	7
β-strand	506	1	7
α-helix	507-508	2
β-strand	509	1	8
α-helix	513-524	12
β-strand	528-530	3	9
β-strand	538	1	9
α-helix	542-551	10
β-strand	560	1	10
α-helix	561-563	3
α-helix	564-568	5
β-strand	579-581	3	9
β-strand	586	1	10
α-helix	592-601	10
α-helix	605-608	4
α-helix	613-625	13
α-helix	632-636	5
α-helix	637-639	3
α-helix	645-651	7
β-strand	659	1	8
α-helix	664-667	4
α-helix	679-684	6
α-helix	693-697	5
α-helix	705-711	7
α-helix	720-725	6
α-helix	731-750	20
β-strand	758-763	6	1
α-helix	770-775	6
α-helix	780-790	11
α-helix	795-797	3
α-helix	809-816	8
β-strand	820	1	11
β-strand	827	1	11
β-strand	837-840	4	12
β-strand	855-858	4	12
α-helix	860-865	6
α-helix	873-888	16
α-helix	894-900	7
α-helix	902-904	3
α-helix	918-939	22
α-helix	942	1
β-strand	943	1	13
α-helix	944	1
β-strand	949	1	13
β-strand	954-959	6	1
α-helix	960-969	10
α-helix	982-999	18
α-helix	1081-1086	6
β-strand	1093-1096	4	1
α-helix	1097-1098	2
β-strand	1111	1	14
β-strand	1120	1	15
α-helix	1128-1131	4
β-strand	1133	1	14
β-strand	1134	1	15
α-helix	1137-1138	2
β-strand	1139-1150	12	16
β-strand	1157-1167	11	16
α-helix	1171-1176	6
α-helix	1178-1184	7
β-strand	1188	1	16
α-helix	1192-1194	3
β-strand	1196-1198	3	16
β-strand	1203-1205	3	3
α-helix	1207-1209	3
β-strand	1211-1214	4	3
β-strand	1220-1222	3	3
α-helix	1230-1239	10
α-helix	1253-1260	8
α-helix	1264-1276	13
α-helix	1277-1281	5
α-helix	1284-1295	12
α-helix	1302-1312	11
α-helix	1313-1316	4
β-strand	1319	1	3
β-strand	1324-1325	2	17
α-helix	1329	1
β-strand	1330-1331	2	17
α-helix	1332-1333	2
β-strand	1336	1	3
α-helix	1342-1344	3
β-strand	1346-1350	5	3
β-strand	1357-1361	5	3
α-helix	1362-1364	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cas9/Csn1	A	protein	1372	Streptococcus pyogenes	Q99ZW2 (AlphaFold model)
single guide RNA	B	RNA	102	synthetic construct
5' product of target strand DNA	C	DNA	13	synthetic construct
non-target strand DNA	D	DNA	40	synthetic construct
3' product of target strand DNA	c	DNA	27	synthetic construct

Sequence of entity 1 (A), FASTA

>6O0Y_1 CRISPR-associated endonuclease Cas9/Csn1 (chains A)
GAASMDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSG
ETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERH
PIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNP
DNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNG
LFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNL
SDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSK
NGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHL
GELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPW
NFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRK
PAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHD
LLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRY
TGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQ
GDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKN
SRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDY
DVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRK
FDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVI
TLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVY
DVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDK
GRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDS
PTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLII
KLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQ
LFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLT
NLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD

Sequence of entity 2 (B), FASTA

>6O0Y_2 single guide RNA (chains B)
GGGGCGCAUAAAGAUGAGACGCGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAG
UCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUGC

Sequence of entity 3 (C), FASTA

>6O0Y_3 5' product of target strand DNA (chains C)
CTAATCGCCAGCG

Sequence of entity 4 (D), FASTA

>6O0Y_4 non-target strand DNA (chains D)
CCAGTGCGTAGGCGCATAAAGATGAGACGCTGGCGATTAG

Sequence of entity 5 (c), FASTA

>6O0Y_5 3' product of target strand DNA (chains c)
TCTCATCTTTATGCGCCTACGCACTGG

Primary citation

Cryo-EM structures reveal coordinated domain motions that govern DNA cleavage by Cas9. Zhu, X., Clarke, R., Puppala, A.K. et al. Nat Struct Mol Biol (2019) 26:679-685. DOI 10.1038/s41594-019-0258-2 · PubMed

Other PDB entries of the same protein (UniProt Q99ZW2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SCA 1.67 Å, Rec3 Domain from S. pyogenes Cas9
6O56 1.9 Å, HNH Nuclease from S. pyogenes Cas9
5B2R 2.0 Å, Crystal structure of the Streptococcus pyogenes Cas9 VQR variant in complex with sgRNA…
5FQ5 2.14 Å, Crystal structure of Cas9-sgRNA-DNA complex solved by native SAD phasing
7OXA 2.15 Å, Target-bound SpCas9 complex with AAVS1 chimeric RNA-DNA guide
5B2S 2.2 Å, Crystal structure of the Streptococcus pyogenes Cas9 EQR variant in complex with sgRNA…
5B2T 2.2 Å, Crystal structure of the Streptococcus pyogenes Cas9 VRER variant in complex with sgRNA…
7QQV 2.25 Å, SpCas9 bound to FANCF off-target3 DNA substrate
7QQZ 2.25 Å, SpCas9 bound to FANCF off-target7 DNA substrate
7QR0 2.3 Å, SpCas9 bound to TRAC off-target1 DNA substrate
4UN4 2.37 Å, Crystal structure of Cas9 bound to PAM-containing DNA target with mismatches at…
4UN5 2.4 Å, Crystal structure of Cas9 bound to PAM-containing DNA target containing mismatches at…

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6O0Y is part of these collections:

CRISPR and genome editing

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