4OO8: Streptococcus pyogenes Cas9

Crystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNA. Determined by X-ray diffraction at 2.5 Å resolution. Released 26 Feb 2014.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Streptococcus pyogenes serotype M1
Chains: 6
Atoms: 24,153
Mol. weight: 395.17 kDa
Released: 26 Feb 2014

Explore 4OO8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4OO8 contains 156 α-helices and 101 β-strands across 2 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: 85 helices, 52 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	34-36	3	3
β-strand	42-46	5	2
β-strand	48-52	5	1
α-helix	54-56	3
α-helix	60-93	34
α-helix	97-101	5
α-helix	122-131	10
α-helix	135-144	10
α-helix	151-163	13
β-strand	167	1	4
α-helix	181-195	15
α-helix	208-212	5
α-helix	218-227	10
α-helix	237-246	10
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	344-346	3
α-helix	347-351	5
α-helix	359-360	2
α-helix	361-365	5
α-helix	369-382	14
α-helix	387-394	8
α-helix	407-409	3
β-strand	411	1	4
α-helix	412-425	14
α-helix	431-435	5
α-helix	437-445	9
β-strand	467	1	6
α-helix	472-473	2
α-helix	478-481	4
β-strand	482	1	6
α-helix	484-493	10
α-helix	497	1
β-strand	498	1	7
α-helix	499	1
β-strand	506	1	7
β-strand	507-509	3	8
α-helix	513-524	12
β-strand	528-530	3	9
β-strand	538-539	2	9
α-helix	542-548	7
α-helix	549-553	5
β-strand	560	1	10
α-helix	561-563	3
α-helix	564-570	7
β-strand	579-581	3	9
β-strand	586	1	10
α-helix	592-601	10
α-helix	604-608	5
α-helix	610-612	3
α-helix	613-625	13
α-helix	629-635	7
α-helix	637-639	3
α-helix	645-653	9
β-strand	659-663	5	8
α-helix	664-668	5
α-helix	670-672	3
α-helix	679-684	6
α-helix	693-698	6
α-helix	704-709	6
α-helix	720-726	7
α-helix	731-750	20
α-helix	754-756	3
β-strand	758-763	6	1
α-helix	764-767	4
α-helix	776-791	16
α-helix	804-807	4
α-helix	809-816	8
β-strand	820	1	11
β-strand	827	1	11
α-helix	828-829	2
β-strand	837-839	3	12
α-helix	852-854	3
β-strand	856-858	3	12
α-helix	862-864	3
α-helix	873-888	16
α-helix	894-900	7
α-helix	902-905	4
α-helix	910-918	9
β-strand	922	1	1
α-helix	926-939	14
β-strand	954-958	5	1
α-helix	960-969	10
α-helix	981-1000	20
β-strand	1007	1	1
α-helix	1031-1036	6
α-helix	1037-1041	5
α-helix	1042-1044	3
β-strand	1064-1066	3	13
β-strand	1072-1075	4	13
α-helix	1079-1086	8
β-strand	1093-1096	4	1
β-strand	1099	1	14
β-strand	1106	1	15
α-helix	1109-1110	2
β-strand	1111	1	16
α-helix	1112-1113	2
β-strand	1120-1121	2	16
α-helix	1128-1131	4
β-strand	1133-1134	2	16
β-strand	1137	1	15
α-helix	1138	1
β-strand	1139-1151	13	17
β-strand	1156-1167	12	17
α-helix	1171-1176	6
α-helix	1178-1183	6
β-strand	1188	1	17
α-helix	1192-1194	3
β-strand	1196-1198	3	17
β-strand	1200	1	14
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	1230-1241	12
α-helix	1250-1253	4
α-helix	1255-1262	8
α-helix	1266-1276	11
α-helix	1277-1281	5
α-helix	1284-1296	13
α-helix	1302-1309	8
α-helix	1310-1314	5
β-strand	1319	1	3
β-strand	1324-1326	3	18
β-strand	1329-1331	3	18
β-strand	1336	1	3
α-helix	1341-1344	4
β-strand	1346-1350	5	3
β-strand	1357-1361	5	3
α-helix	1362-1365	4

Chain D: 71 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	19
β-strand	15-21	7	19
β-strand	29-33	5	20
β-strand	35-36	2	21
β-strand	42-46	5	20
β-strand	48-52	5	19
α-helix	54-56	3
α-helix	60-93	34
α-helix	97-101	5
α-helix	122-131	10
α-helix	135-144	10
α-helix	148-150	3
α-helix	151-163	13
β-strand	167	1	22
α-helix	173-175	3
α-helix	181-195	15
α-helix	208-212	5
α-helix	218-226	9
α-helix	237-245	9
β-strand	251	1	23
β-strand	263	1	23
α-helix	271-282	12
α-helix	284-286	3
α-helix	287-305	19
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	387-394	8
α-helix	405-409	5
β-strand	411	1	22
α-helix	412-423	12
α-helix	432-435	4
α-helix	437-445	9
β-strand	467	1	24
α-helix	478-481	4
β-strand	482	1	24
α-helix	484-493	10
α-helix	497	1
β-strand	498	1	25
α-helix	499	1
β-strand	506	1	25
α-helix	507-508	2
β-strand	509	1	26
α-helix	513-524	12
β-strand	528-531	4	27
β-strand	538	1	27
α-helix	542-548	7
α-helix	549-553	5
β-strand	560	1	28
α-helix	561-563	3
α-helix	564-573	10
β-strand	578-581	4	27
β-strand	586	1	28
α-helix	592-600	9
α-helix	604-608	5
α-helix	610-612	3
α-helix	613-625	13
α-helix	629-634	6
α-helix	645-653	9
β-strand	659	1	26
α-helix	664-668	5
α-helix	679-684	6
α-helix	693-696	4
α-helix	704-709	6
α-helix	720-725	6
α-helix	731-733	3
α-helix	734-750	17
α-helix	754-756	3
β-strand	758-763	6	19
α-helix	920-939	20
β-strand	943	1	29
β-strand	949	1	29
β-strand	954-959	6	19
α-helix	960-969	10
α-helix	981-1000	20
β-strand	1007	1	19
α-helix	1039-1046	8
β-strand	1064-1066	3	30
β-strand	1072-1075	4	30
α-helix	1079-1086	8
β-strand	1093-1096	4	19
β-strand	1099	1	31
β-strand	1106	1	32
α-helix	1109-1110	2
β-strand	1111	1	33
α-helix	1112-1113	2
α-helix	1119	1
β-strand	1120-1121	2	33
α-helix	1128-1131	4
β-strand	1133-1134	2	33
β-strand	1137	1	32
α-helix	1138	1
β-strand	1139-1151	13	34
β-strand	1156-1167	12	34
α-helix	1171-1176	6
α-helix	1178-1185	8
β-strand	1188	1	34
α-helix	1192-1194	3
β-strand	1196-1198	3	34
β-strand	1200	1	31
β-strand	1202-1205	4	21
β-strand	1211-1216	6	21
β-strand	1219-1222	4	21
α-helix	1230-1238	9
α-helix	1250-1259	10
α-helix	1265-1276	12
α-helix	1277-1281	5
α-helix	1284-1295	12
α-helix	1302-1312	11
α-helix	1313-1315	3
β-strand	1319	1	21
β-strand	1324-1326	3	35
β-strand	1329-1331	3	35
α-helix	1332-1333	2
β-strand	1336	1	21
α-helix	1340-1344	5
β-strand	1346-1350	5	21
β-strand	1357-1361	5	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cas9/Csn1	A, D	protein	1372	Streptococcus pyogenes serotype M1	Q99ZW2 (AlphaFold model)
RNA (97-mer)	B, E	RNA	98
DNA (5'-d(cpcpapgpcpcpapapgpcpgpcpapcpcptpapaptptptpcp*c)-3')	C, F	DNA	23

Sequence of entity 1 (A, D), FASTA

>4OO8_1 CRISPR-associated endonuclease Cas9/Csn1 (chains A, D)
GSGHMDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSG
ETAEATRLKRTARRRYTRRKNRILYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERH
PIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNP
DNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNG
LFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNL
SDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSK
NGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHL
GELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPW
NFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRK
PAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIEEFDSVEISGVEDRFNASLGTYHD
LLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRY
TGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQ
GDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKN
SRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDY
DVDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRK
FDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVI
TLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVY
DVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDK
GRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDS
PTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLII
KLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQ
LFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLT
NLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD

Sequence of entity 2 (B, E), FASTA

>4OO8_2 RNA (97-MER) (chains B, E)
GGAAAUUAGGUGCGCUUGGCGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUC
CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUU

Sequence of entity 3 (C, F), FASTA

>4OO8_3 DNA (5'-D(*CP*CP*AP*GP*CP*CP*AP*AP*GP*CP*GP*CP*AP*CP*CP*TP*AP*AP*TP*TP*TP*CP*C)-3') (chains C, F)
CCAGCCAAGCGCACCTAATTTCC

Primary citation

Crystal structure of Cas9 in complex with guide RNA and target DNA. Nishimasu, H., Ran, F.A., Hsu, P.D. et al. Cell (2014) 156:935-949. DOI 10.1016/j.cell.2014.02.001 · 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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4OO8 is part of these collections:

CRISPR and genome editing

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