7ZO1: SpCas9

SpCas9 bound to CD34 off-target9 DNA substrate. Determined by X-ray diffraction at 2.4 Å resolution. Released 26 Oct 2022.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: synthetic construct, Streptococcus pyogenes
Chains: 4
Atoms: 12,407
Mol. weight: 198.66 kDa
Ligands: MG
Released: 26 Oct 2022

Explore 7ZO1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZO1 contains 71 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 B: 71 helices, 54 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	1
β-strand	15-21	7	1
α-helix	26-28	3
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	181-195	15
α-helix	208-212	5
α-helix	218-227	10
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	287-300	14
α-helix	316-342	27
α-helix	347-351	5
α-helix	359-363	5
α-helix	369-382	14
α-helix	388-394	7
α-helix	405-409	5
β-strand	411	1	4
α-helix	412-426	15
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	484-493	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	629-636	8
α-helix	637-639	3
α-helix	645-652	8
β-strand	659-663	5	8
α-helix	664	1
α-helix	665-669	5
β-strand	671	1	11
β-strand	678	1	11
α-helix	679-684	6
α-helix	693-697	5
α-helix	704-711	8
α-helix	720-725	6
α-helix	731-750	20
α-helix	754-756	3
β-strand	758-763	6	1
α-helix	926-939	14
β-strand	943	1	12
β-strand	949	1	12
β-strand	954-957	4	1
α-helix	960-970	11
α-helix	981-1000	20
α-helix	1002-1004	3
α-helix	1005-1008	4
β-strand	1009	1	1
α-helix	1044-1046	3
β-strand	1049-1050	2	13
β-strand	1058-1059	2	13
β-strand	1063-1065	3	14
β-strand	1072-1075	4	14
α-helix	1079-1086	8
β-strand	1093-1096	4	1
β-strand	1099	1	15
β-strand	1106	1	16
β-strand	1111	1	17
α-helix	1112-1113	2
β-strand	1120	1	18
α-helix	1128-1131	4
β-strand	1133	1	17
β-strand	1134	1	18
β-strand	1137	1	16
α-helix	1138	1
β-strand	1139-1151	13	19
β-strand	1156-1167	12	19
α-helix	1171-1176	6
α-helix	1178-1184	7
β-strand	1187-1188	2	19
α-helix	1192-1194	3
β-strand	1196-1199	4	19
β-strand	1200	1	15
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	1230-1240	11
α-helix	1250-1261	12
α-helix	1265-1276	12
α-helix	1277-1281	5
α-helix	1284-1296	13
α-helix	1297-1299	3
α-helix	1302-1312	11
α-helix	1313-1315	3
β-strand	1319	1	3
β-strand	1324-1326	3	20
β-strand	1329-1331	3	20
β-strand	1336	1	3
α-helix	1341-1344	4
β-strand	1346-1350	5	3
β-strand	1357-1361	5	3
α-helix	1362-1364	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CD34 sgRNA	A	RNA	85	synthetic construct
CRISPR-associated endonuclease Cas9/Csn1	B	protein	1368	Streptococcus pyogenes	Q99ZW2 (AlphaFold model)
CD34 off-target9 DNA target strand	C	DNA	28	synthetic construct
CD34 off-target9 DNA non-target strand	D	DNA	12	synthetic construct

Sequence of entity 1 (A), FASTA

>7ZO1_1 CD34 sgRNA (chains A)
AGGAUAGGAGAAGAUGAUGUAUAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUA
GUCCGUUAUCAACUUGAAAAAGUGA

Sequence of entity 2 (B), FASTA

>7ZO1_2 CRISPR-associated endonuclease Cas9/Csn1 (chains B)
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 3 (C), FASTA

>7ZO1_3 CD34 off-target9 DNA target strand (chains C)
CAATACCATATTCATCATCTTCCCTATC

Sequence of entity 4 (D), FASTA

>7ZO1_4 CD34 off-target9 DNA non-target strand (chains D)
AATATGGTATTG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

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

Primary citation

Structural basis for Cas9 off-target activity. Pacesa, M., Lin, C.H., Clery, A. et al. Cell (2022) 185:4067-4081.e21. DOI 10.1016/j.cell.2022.09.026 · 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…

Browse structure collections

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