7OXA: CRISPR-associated endonuclease Cas9/Csn1

Target-bound SpCas9 complex with AAVS1 chimeric RNA-DNA guide. Determined by X-ray diffraction at 2.15 Å resolution. Released 15 Sept 2021.

Method: X-ray diffraction
Resolution: 2.15 Å
Organisms: synthetic construct, Streptococcus pyogenes serotype M1
Chains: 4
Atoms: 13,928
Mol. weight: 197.79 kDa
Ligands: MG
Released: 15 Sept 2021

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

Secondary structure: helices and β-sheets

7OXA contains 82 α-helices and 56 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: 82 helices, 56 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
α-helix	253-256	4
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	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	407-409	3
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	564-573	10
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	645-653	9
β-strand	659-663	5	8
α-helix	664-668	5
α-helix	679-684	6
α-helix	693-698	6
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	777-790	14
α-helix	795-798	4
α-helix	804-807	4
α-helix	809-816	8
β-strand	820	1	11
β-strand	827	1	11
α-helix	830-835	6
β-strand	837-840	4	12
α-helix	852-854	3
β-strand	855-858	4	12
α-helix	861-864	4
α-helix	873-888	16
α-helix	894-900	7
α-helix	902-904	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	960-970	11
α-helix	981-1000	20
α-helix	1002-1004	3
α-helix	1005-1008	4
β-strand	1009	1	1
α-helix	1033-1040	8
α-helix	1044-1046	3
β-strand	1049-1051	3	14
β-strand	1057-1059	3	14
β-strand	1063-1065	3	15
β-strand	1072-1075	4	15
α-helix	1079-1088	10
β-strand	1093-1096	4	1
β-strand	1099	1	16
β-strand	1106	1	17
β-strand	1111	1	18
α-helix	1112-1113	2
β-strand	1120	1	19
α-helix	1128-1131	4
β-strand	1133	1	18
β-strand	1134	1	19
β-strand	1137	1	17
α-helix	1138	1
β-strand	1139-1151	13	20
β-strand	1156-1167	12	20
α-helix	1171-1176	6
α-helix	1178-1184	7
β-strand	1188	1	20
α-helix	1192-1194	3
β-strand	1196-1199	4	20
β-strand	1200	1	16
β-strand	1203-1205	3	3
β-strand	1211-1214	4	3
β-strand	1220-1222	3	3
α-helix	1230-1239	10
α-helix	1253-1261	9
α-helix	1265-1276	12
α-helix	1277-1281	5
α-helix	1284-1296	13
α-helix	1302-1312	11
β-strand	1319	1	3
β-strand	1324-1326	3	21
β-strand	1329-1331	3	21
α-helix	1332-1335	4
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
chimeric RNA-DNA guide	A	NA-hybrid	81	synthetic construct
CRISPR-associated endonuclease Cas9/Csn1	B	protein	1372	Streptococcus pyogenes serotype M1	Q99ZW2 (AlphaFold model)
AAVS1 target DNA strand	C	DNA	28	synthetic construct
AAVS1 non-target DNA strand	D	DNA	12	synthetic construct

Sequence of entity 1 (A), FASTA

>7OXA_1 chimeric RNA-DNA guide (chains A)
GGGGCCACTAGGGACAGGAUGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUC
CGUUAUCAACUUGAAAAAGUG

Sequence of entity 2 (B), FASTA

>7OXA_2 CRISPR-associated endonuclease Cas9/Csn1 (chains B)
GAASMDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSG
ETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERH
PIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNP
DNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNG
LFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNL
SDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSK
NGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHL
GELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPW
NFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRK
PAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHD
LLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRY
TGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQ
GDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKN
SRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDY
DVDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRK
FDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVI
TLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVY
DVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDK
GRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDS
PTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLII
KLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQ
LFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLT
NLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD

Sequence of entity 3 (C), FASTA

>7OXA_3 AAVS1 target DNA strand (chains C)
CAATACCAATCCTGTCCCTAGTGGCCCC

Sequence of entity 4 (D), FASTA

>7OXA_4 AAVS1 non-target DNA strand (chains D)
GGATTGGTATTG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

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

Primary citation

Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells. Donohoue, P.D., Pacesa, M., Lau, E. et al. Mol Cell (2021) 81:3637-3649.e5. DOI 10.1016/j.molcel.2021.07.035 · 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
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…
7QQS 2.4 Å, SpCas9 bound to FANCF on-target DNA substrate

Browse structure collections

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