4ZT0: Catalytically-active Streptococcus pyogenes Cas9

Crystal structure of catalytically-active Streptococcus pyogenes Cas9 in complex with single-guide RNA at 2.9 Angstrom resolution. Determined by X-ray diffraction at 2.9 Å resolution. Released 8 Jul 2015.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Streptococcus pyogenes
Chains: 4
Atoms: 23,790
Mol. weight: 374.61 kDa
Released: 8 Jul 2015

Explore 4ZT0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4ZT0 contains 156 α-helices and 110 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: 81 helices, 56 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	97-102	6
α-helix	122-131	10
α-helix	135-144	10
α-helix	151-163	13
β-strand	167	1	4
α-helix	176-178	3
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
α-helix	253-256	4
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	359-363	5
α-helix	369-382	14
α-helix	389-394	6
α-helix	405-409	5
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	478-481	4
β-strand	482	1	6
α-helix	484-495	12
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	540-541	2
α-helix	542-548	7
α-helix	549-553	5
β-strand	560	1	10
α-helix	561-564	4
α-helix	565-569	5
β-strand	579-580	2	9
β-strand	586	1	10
α-helix	592-601	10
α-helix	606-608	3
α-helix	613-625	13
α-helix	629-635	7
α-helix	646-653	8
β-strand	659-663	5	8
α-helix	664-668	5
α-helix	679-684	6
α-helix	693-698	6
α-helix	704-710	7
α-helix	714	1
α-helix	720-725	6
α-helix	731-750	20
α-helix	754-756	3
β-strand	758-763	6	1
α-helix	775-791	17
α-helix	795-798	4
α-helix	805-807	3
α-helix	809-816	8
β-strand	820	1	11
β-strand	827	1	11
β-strand	837-840	4	12
α-helix	852-854	3
β-strand	855-858	4	12
α-helix	861-864	4
α-helix	872	1
α-helix	873-888	16
α-helix	894-900	7
α-helix	903-905	3
α-helix	910-921	12
α-helix	926-939	14
β-strand	943	1	13
β-strand	949	1	13
β-strand	954-958	5	1
α-helix	960-969	10
α-helix	981-1000	20
α-helix	1002-1004	3
α-helix	1005-1008	4
β-strand	1022	1	14
β-strand	1037	1	14
α-helix	1042-1044	3
β-strand	1049-1051	3	15
β-strand	1057-1059	3	15
β-strand	1063-1065	3	16
β-strand	1072-1075	4	16
α-helix	1078-1088	11
β-strand	1093-1096	4	1
α-helix	1097-1098	2
β-strand	1099	1	17
β-strand	1106	1	18
β-strand	1111	1	19
α-helix	1112-1113	2
β-strand	1120-1121	2	19
α-helix	1128-1131	4
β-strand	1133-1134	2	19
β-strand	1137	1	18
α-helix	1138	1
β-strand	1139-1151	13	20
β-strand	1156-1167	12	20
α-helix	1168-1176	9
α-helix	1178-1185	8
β-strand	1188	1	20
β-strand	1196-1198	3	20
β-strand	1200	1	17
β-strand	1202-1205	4	3
α-helix	1207-1209	3
β-strand	1211-1214	4	3
β-strand	1220-1222	3	3
α-helix	1230-1240	11
α-helix	1249-1261	13
α-helix	1264-1276	13
α-helix	1277-1281	5
α-helix	1284-1296	13
α-helix	1302-1312	11
α-helix	1313-1315	3
β-strand	1319	1	3
β-strand	1324-1326	3	21
β-strand	1329-1331	3	21
β-strand	1336	1	3
α-helix	1340-1344	5
β-strand	1346-1350	5	3
β-strand	1357-1361	5	3
α-helix	1362-1364	3

Chain C: 75 helices, 54 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	22
β-strand	15-21	7	22
β-strand	29-33	5	23
β-strand	34-36	3	24
β-strand	42-46	5	23
β-strand	48-52	5	22
α-helix	54-56	3
α-helix	60-93	34
α-helix	97-102	6
α-helix	122-131	10
α-helix	135-144	10
α-helix	151-163	13
β-strand	167	1	25
α-helix	176-178	3
α-helix	181-195	15
α-helix	208-212	5
α-helix	218-227	10
α-helix	237-246	10
β-strand	251	1	26
α-helix	253-256	4
β-strand	263	1	26
α-helix	271-282	12
α-helix	284-286	3
α-helix	287-304	18
α-helix	316-342	27
α-helix	347-351	5
α-helix	359-363	5
α-helix	369-382	14
α-helix	389-394	6
α-helix	405-409	5
β-strand	411	1	25
α-helix	412-425	14
α-helix	431-435	5
α-helix	437-445	9
β-strand	467	1	27
α-helix	478-481	4
β-strand	482	1	27
α-helix	484-495	12
β-strand	498	1	28
β-strand	506	1	28
β-strand	507-509	3	29
α-helix	513-524	12
β-strand	528-530	3	30
β-strand	538-539	2	30
α-helix	540-541	2
α-helix	542-548	7
α-helix	549-553	5
β-strand	560	1	31
α-helix	561-564	4
α-helix	565-569	5
β-strand	579-580	2	30
β-strand	586	1	31
α-helix	592-601	10
α-helix	605-608	4
α-helix	613-625	13
α-helix	629-635	7
α-helix	637-640	4
α-helix	646-653	8
β-strand	659-663	5	29
α-helix	664-668	5
β-strand	671	1	32
β-strand	678	1	32
α-helix	679-684	6
α-helix	694-699	6
α-helix	704-713	10
α-helix	720-725	6
α-helix	731-750	20
α-helix	754-756	3
β-strand	758-763	6	22
α-helix	776-791	16
α-helix	795-798	4
α-helix	810-816	7
β-strand	820	1	33
β-strand	827	1	33
β-strand	837-840	4	34
α-helix	852-854	3
β-strand	855-858	4	34
α-helix	861-864	4
α-helix	876-883	8
α-helix	894-898	5
α-helix	910-921	12
α-helix	926-939	14
β-strand	954-958	5	22
α-helix	960-969	10
α-helix	981-1000	20
α-helix	1002-1004	3
α-helix	1005-1008	4
β-strand	1049	1	35
β-strand	1059	1	35
β-strand	1063-1065	3	36
β-strand	1072-1075	4	36
α-helix	1078-1087	10
β-strand	1093-1096	4	22
β-strand	1099	1	37
β-strand	1106	1	38
β-strand	1111	1	39
α-helix	1112-1113	2
β-strand	1120-1121	2	39
α-helix	1128-1131	4
β-strand	1133-1134	2	39
β-strand	1137	1	38
α-helix	1138	1
β-strand	1139-1151	13	40
β-strand	1156-1167	12	40
α-helix	1168-1176	9
α-helix	1178-1185	8
β-strand	1188	1	40
α-helix	1192-1194	3
β-strand	1196-1198	3	40
β-strand	1200	1	37
β-strand	1202-1205	4	24
α-helix	1207-1209	3
β-strand	1211-1214	4	24
β-strand	1220-1222	3	24
α-helix	1230-1241	12
α-helix	1249-1261	13
α-helix	1264-1276	13
α-helix	1277-1281	5
α-helix	1284-1296	13
α-helix	1302-1312	11
α-helix	1313-1315	3
β-strand	1319	1	24
β-strand	1324-1326	3	41
β-strand	1329-1331	3	41
β-strand	1336	1	24
α-helix	1341-1344	4
β-strand	1346-1350	5	24
β-strand	1357-1361	5	24
α-helix	1362-1364	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cas9	A, C	protein	1369	Streptococcus pyogenes	Q99ZW2 (AlphaFold model)
single-guide RNA	B, D	RNA	85	Streptococcus pyogenes

Sequence of entity 1 (A, C), FASTA

>4ZT0_1 CRISPR-associated endonuclease Cas9 (chains A, C)
SMDKKYSIGLDIGTNSVGWAVITDDYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETA
EATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIF
GNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNS
DVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFG
NLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDA
ILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGY
AGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGEL
HAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFE
EVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAF
LSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLK
IIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGW
GRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDS
LHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRE
RMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVD
HIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDN
LTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLK
SKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVR
KMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRD
FATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTV
AYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLP
KYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFV
EQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLG
APAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD

Sequence of entity 2 (B, D), FASTA

>4ZT0_2 single-guide RNA (chains B, D)
GGCGCAUAAAGAUGAGACGCGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUC
CGUUAUCAACUUGAAAAAGUGUUCG

Primary citation

A Cas9-guide RNA complex preorganized for target DNA recognition. Jiang, F., Zhou, K., Ma, L. et al. Science (2015) 348:1477-1481. DOI 10.1126/science.aab1452 · 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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4ZT0 is part of these collections:

CRISPR and genome editing

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