5Y36: SpCas9-sgRNA-DNA ternary complex

Cryo-EM structure of SpCas9-sgRNA-DNA ternary complex. Determined by electron microscopy at 5.2 Å resolution. Released 6 Dec 2017.

Method: Electron microscopy
Resolution: 5.2 Å
Organisms: Streptococcus pyogenes serotype M1, Mus musculus
Chains: 4
Atoms: 14,960
Mol. weight: 215.8 kDa
Ligands: MG
Released: 6 Dec 2017

Explore 5Y36 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Y36 contains 79 α-helices and 54 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: 79 helices, 54 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	1
β-strand	15-22	8	1
β-strand	25	1	1
β-strand	29-31	3	2
α-helix	33-34	2
β-strand	35-36	2	3
β-strand	44-46	3	2
β-strand	49-52	4	1
α-helix	59-93	35
α-helix	97-102	6
α-helix	108-110	3
α-helix	122-125	4
α-helix	135-143	9
α-helix	151-163	13
β-strand	167	1	4
α-helix	182-195	14
α-helix	200-202	3
α-helix	208-213	6
α-helix	218-228	11
α-helix	237-245	9
β-strand	251	1	5
β-strand	263	1	5
α-helix	271-282	12
α-helix	284-286	3
α-helix	287-305	19
α-helix	316-342	27
α-helix	347-351	5
α-helix	354-356	3
α-helix	359-364	6
α-helix	369-382	14
α-helix	387-395	9
α-helix	405-407	3
β-strand	411	1	4
α-helix	412-425	14
α-helix	432-445	14
β-strand	467	1	6
α-helix	478-481	4
β-strand	482	1	6
α-helix	484-494	11
β-strand	498	1	7
β-strand	506	1	7
α-helix	507-508	2
β-strand	509	1	8
α-helix	513-525	13
β-strand	528-530	3	9
β-strand	538-539	2	9
α-helix	540-541	2
α-helix	542-548	7
α-helix	549-553	5
β-strand	558-560	3	10
α-helix	561-563	3
α-helix	564-568	5
α-helix	569-571	3
β-strand	579-581	3	9
β-strand	586-590	5	10
α-helix	593-601	9
α-helix	612-625	14
α-helix	629-638	10
α-helix	645-651	7
β-strand	659	1	8
α-helix	664	1
α-helix	665-669	5
α-helix	679-684	6
α-helix	693-698	6
α-helix	705-710	6
α-helix	720-723	4
α-helix	731-750	20
α-helix	754-755	2
β-strand	756-763	8	1
β-strand	767	1	11
α-helix	777-791	15
α-helix	795-798	4
α-helix	809-817	9
β-strand	820	1	12
β-strand	827	1	12
α-helix	830-832	3
β-strand	838-840	3	13
β-strand	850	1	11
α-helix	852-854	3
β-strand	855-857	3	13
α-helix	862-864	3
α-helix	873-888	16
α-helix	894-898	5
α-helix	902-905	4
α-helix	911-916	6
α-helix	928-939	12
β-strand	955-957	3	1
α-helix	960-962	3
α-helix	964-969	6
α-helix	976-978	3
α-helix	982-999	18
α-helix	1020-1022	3
α-helix	1024-1028	5
α-helix	1038-1046	9
β-strand	1049	1	14
β-strand	1059	1	14
α-helix	1076-1080	5
α-helix	1081-1087	7
β-strand	1093-1096	4	1
α-helix	1097-1098	2
β-strand	1099	1	15
β-strand	1107-1110	4	16
β-strand	1121	1	17
β-strand	1133	1	17
β-strand	1134-1135	2	16
β-strand	1139-1146	8	18
β-strand	1150-1151	2	19
β-strand	1156-1157	2	19
β-strand	1160	1	20
β-strand	1161-1167	7	18
α-helix	1168-1174	7
α-helix	1178-1185	8
α-helix	1192-1194	3
β-strand	1196-1198	3	18
β-strand	1200	1	15
β-strand	1203-1206	4	3
β-strand	1210-1214	5	3
α-helix	1219	1
β-strand	1220-1221	2	3
α-helix	1231-1241	11
α-helix	1250-1261	12
α-helix	1265-1280	16
α-helix	1287-1296	10
α-helix	1302-1309	8
α-helix	1310-1316	7
β-strand	1325	1	21
β-strand	1330	1	21
α-helix	1331-1333	3
β-strand	1336	1	3
α-helix	1342-1344	3
β-strand	1345-1350	6	3
β-strand	1357-1359	3	3
β-strand	1366	1	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cas9/Csn1	A	protein	1368	Streptococcus pyogenes serotype M1	Q99ZW2 (AlphaFold model)
single-guide RNA	B	RNA	99	Mus musculus
complementary DNA strand	C	DNA	41	Mus musculus
non-complementary DNA strand	D	DNA	41	Mus musculus

Sequence of entity 1 (A), FASTA

>5Y36_1 CRISPR-associated endonuclease Cas9/Csn1 (chains A)
MDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAE
ATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFG
NIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSD
VDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGN
LIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAI
LLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYA
GYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELH
AILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEE
VVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFL
SGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKI
IKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWG
RLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSL
HEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRER
MKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDA
IVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNL
TKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKS
KLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRK
MIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDF
ATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVA
YSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPK
YSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVE
QHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGA
PAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD

Sequence of entity 2 (B), FASTA

>5Y36_2 single-guide RNA (chains B)
GGUACCGCUCCAGUCGUUCAUGGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAG
UCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCU

Sequence of entity 3 (C), FASTA

>5Y36_3 complementary DNA strand (chains C)
ACATTTTCGGGATGGTCCTCATGAACGACTGGAGCGGTAAT

Sequence of entity 4 (D), FASTA

>5Y36_4 non-complementary DNA strand (chains D)
ATTACCGCTCCAGTCGTTCATGAGGACCATCCCGAAAATGT

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3

Primary citation

Structural insights into DNA cleavage activation of CRISPR-Cas9 system. Huai, C., Li, G., Yao, R. et al. Nat Commun (2017) 8:1375-1375. DOI 10.1038/s41467-017-01496-2 · 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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5Y36 is part of these collections:

CRISPR and genome editing

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