4CMP: S. pyogenes Cas9

Crystal structure of S. pyogenes Cas9. Determined by X-ray diffraction at 2.62 Å resolution. Released 12 Feb 2014.

Method: X-ray diffraction
Resolution: 2.62 Å
Organism: STREPTOCOCCUS PYOGENES
Chains: 2
Atoms: 19,091
Mol. weight: 318.48 kDa
Ligands: MG
Released: 12 Feb 2014

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

Secondary structure: helices and β-sheets

4CMP contains 140 α-helices and 84 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: 70 helices, 40 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	1	3
β-strand	42-46	5	2
β-strand	48-52	5	1
α-helix	59-63	5
α-helix	68-93	26
α-helix	97-100	4
α-helix	122-131	10
α-helix	135-144	10
α-helix	151-163	13
β-strand	167	1	4
α-helix	176-179	4
α-helix	181-195	15
α-helix	208-213	6
α-helix	218-226	9
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	287-306	20
α-helix	316-342	27
α-helix	345-352	8
α-helix	359-363	5
α-helix	369-383	15
α-helix	388-395	8
β-strand	411	1	4
α-helix	412-426	15
α-helix	431-445	15
α-helix	506-508	3
β-strand	509	1	6
α-helix	513-524	12
α-helix	542-548	7
α-helix	549-553	5
α-helix	561-566	6
α-helix	592-601	10
α-helix	604-608	5
α-helix	610-612	3
α-helix	613-625	13
α-helix	629-636	8
α-helix	637-639	3
α-helix	645-653	9
β-strand	659	1	6
α-helix	664	1
α-helix	665-669	5
α-helix	679-683	5
α-helix	693-697	5
α-helix	703-713	11
α-helix	719-725	7
α-helix	731-750	20
α-helix	754-756	3
β-strand	758-763	6	1
α-helix	776-788	13
α-helix	803-807	5
α-helix	809-816	8
β-strand	820	1	7
β-strand	827	1	7
α-helix	830-836	7
β-strand	838-840	3	8
α-helix	852-854	3
β-strand	855-857	3	8
α-helix	876-879	4
α-helix	880-888	9
α-helix	894-901	8
α-helix	910-921	12
α-helix	926-939	14
β-strand	943	1	9
β-strand	949	1	9
β-strand	954-957	4	1
α-helix	960-969	10
α-helix	981-1000	20
α-helix	1002-1004	3
α-helix	1005-1008	4
β-strand	1009	1	1
α-helix	1018-1021	4
α-helix	1042-1046	5
β-strand	1049-1051	3	10
α-helix	1052	1
β-strand	1057-1059	3	10
β-strand	1063-1065	3	11
β-strand	1072-1075	4	11
α-helix	1078-1088	11
β-strand	1093-1096	4	1
β-strand	1099	1	12
β-strand	1139-1145	7	13
β-strand	1162-1167	6	13
α-helix	1168-1176	9
α-helix	1178-1185	8
β-strand	1197-1198	2	13
β-strand	1200	1	12
β-strand	1202-1206	5	3
β-strand	1210-1216	7	3
β-strand	1219-1222	4	3
α-helix	1230-1240	11
α-helix	1264-1276	13
α-helix	1277-1281	5
α-helix	1284-1296	13
α-helix	1302-1311	10
α-helix	1313-1316	4
β-strand	1319	1	3
β-strand	1324-1326	3	14
β-strand	1329-1331	3	14
β-strand	1336	1	3
α-helix	1342-1344	3
β-strand	1346-1350	5	3
α-helix	1351	1
β-strand	1357-1360	4	3

Chain B: 70 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	15
β-strand	15-21	7	15
α-helix	26-28	3
β-strand	29-33	5	16
β-strand	34-36	3	17
β-strand	42-46	5	16
β-strand	48-52	5	15
β-strand	58	1	18
α-helix	59-63	5
α-helix	68-93	26
α-helix	97-100	4
α-helix	122-131	10
α-helix	135-144	10
α-helix	151-163	13
β-strand	167	1	19
α-helix	176-179	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	20
β-strand	263	1	20
α-helix	271-282	12
α-helix	284-286	3
α-helix	287-306	20
α-helix	316-342	27
α-helix	344-352	9
α-helix	354-356	3
α-helix	359-364	6
α-helix	369-383	15
α-helix	388-395	8
β-strand	411	1	19
α-helix	412-426	15
α-helix	431-435	5
α-helix	437-445	9
α-helix	506-508	3
β-strand	509	1	21
α-helix	513-523	11
α-helix	524-526	3
α-helix	544-548	5
α-helix	549-553	5
α-helix	561-569	9
α-helix	592-600	9
α-helix	604-607	4
α-helix	610-625	16
α-helix	629-635	7
α-helix	645-653	9
β-strand	659	1	21
α-helix	664	1
α-helix	665-669	5
α-helix	679-685	7
α-helix	693-697	5
α-helix	703-712	10
α-helix	719-725	7
α-helix	731-750	20
α-helix	754-756	3
β-strand	758-762	5	15
α-helix	774-788	15
α-helix	803-807	5
α-helix	809-816	8
β-strand	820	1	22
β-strand	827	1	22
α-helix	830-833	4
β-strand	839-840	2	23
α-helix	852-854	3
β-strand	855-856	2	23
α-helix	863-866	4
α-helix	880-888	9
α-helix	894-901	8
α-helix	910-921	12
α-helix	926-939	14
β-strand	943	1	24
β-strand	949	1	24
β-strand	954-957	4	15
α-helix	960-970	11
α-helix	982-1000	19
α-helix	1002-1004	3
α-helix	1005-1008	4
β-strand	1009	1	15
α-helix	1018-1021	4
β-strand	1022	1	25
β-strand	1037	1	25
α-helix	1042-1046	5
β-strand	1049-1051	3	26
β-strand	1057-1059	3	26
β-strand	1063-1065	3	27
β-strand	1072-1075	4	27
α-helix	1076-1088	13
β-strand	1093-1096	4	15
β-strand	1099	1	28
β-strand	1101	1	18
β-strand	1139-1146	8	29
β-strand	1161-1167	7	29
α-helix	1168-1175	8
α-helix	1178-1184	7
β-strand	1196-1198	3	29
β-strand	1200	1	28
β-strand	1202-1206	5	17
β-strand	1210-1214	5	17
β-strand	1220-1222	3	17
α-helix	1230-1240	11
α-helix	1258-1261	4
α-helix	1265-1276	12
α-helix	1277-1281	5
α-helix	1284-1296	13
α-helix	1302-1311	10
α-helix	1313-1316	4
β-strand	1319	1	17
β-strand	1324-1326	3	30
β-strand	1329-1331	3	30
β-strand	1336	1	17
α-helix	1341-1344	4
β-strand	1346-1350	5	17
β-strand	1357-1361	5	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease CAS9/CSN1	A, B	protein	1372	STREPTOCOCCUS PYOGENES	Q99ZW2 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4CMP_1 CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 (chains A, B)
GAASMDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSG
ETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERH
PIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNP
DNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNG
LFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNL
SDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSK
NGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHL
GELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPW
NFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRK
PAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHD
LLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRY
TGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQ
GDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKN
SRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDY
DVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRK
FDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVI
TLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVY
DVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDK
GRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDS
PTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLII
KLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQ
LFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLT
NLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation. Jinek, M., Jiang, F., Taylor, D.W. et al. Science (2014) 343:47997. DOI 10.1126/SCIENCE.1247997 · 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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4CMP is part of these collections:

CRISPR and genome editing

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