8SRS: SpRY-Cas9:gRNA complex targeting TAC PAM DNA

SpRY-Cas9:gRNA complex targeting TAC PAM DNA. Determined by electron microscopy at 2.79 Å resolution. Released 1 May 2024.

Method: Electron microscopy
Resolution: 2.79 Å
Organisms: Streptococcus pyogenes, Escherichia phage Lambda
Chains: 5
Atoms: 14,148
Mol. weight: 217.68 kDa
Ligands: MG
Released: 1 May 2024

Explore 8SRS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SRS contains 88 α-helices and 50 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 A: 88 helices, 50 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	1
β-strand	15-22	8	1
α-helix	26-28	3
β-strand	29-33	5	2
β-strand	34-35	2	3
β-strand	42-46	5	2
β-strand	48-52	5	1
α-helix	54-58	5
α-helix	60-93	34
α-helix	97-103	7
α-helix	122-131	10
α-helix	135-144	10
α-helix	151-163	13
β-strand	167	1	4
α-helix	184-195	12
α-helix	209-214	6
α-helix	218-228	11
α-helix	242-245	4
α-helix	252	1
β-strand	253	1	5
α-helix	254	1
β-strand	263	1	5
α-helix	272-275	4
α-helix	289-305	17
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	4
α-helix	412-426	15
α-helix	431-435	5
α-helix	437-445	9
β-strand	467	1	6
α-helix	472-473	2
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
α-helix	507-508	2
β-strand	509	1	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	561-563	3
α-helix	564-569	6
β-strand	579-581	3	9
β-strand	586	1	10
α-helix	592-601	10
α-helix	604-608	5
α-helix	613-625	13
α-helix	629-636	8
α-helix	637-641	5
α-helix	645-651	7
β-strand	659	1	8
α-helix	664	1
α-helix	665-669	5
α-helix	679-684	6
α-helix	693-698	6
α-helix	704-711	8
α-helix	720-725	6
α-helix	732-750	19
α-helix	754-756	3
β-strand	758-763	6	1
α-helix	770-775	6
α-helix	780-791	12
α-helix	795-798	4
α-helix	809-816	8
β-strand	820	1	11
β-strand	827	1	11
α-helix	830-832	3
β-strand	837-840	4	12
α-helix	852-854	3
β-strand	855-858	4	12
α-helix	860-865	6
α-helix	873-887	15
α-helix	894-900	7
α-helix	902-905	4
α-helix	910-913	4
α-helix	918-939	22
β-strand	954-959	6	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	1031-1042	12
α-helix	1043-1046	4
β-strand	1049-1051	3	13
β-strand	1057-1059	3	13
β-strand	1063-1065	3	14
β-strand	1072-1075	4	14
α-helix	1078-1087	10
β-strand	1093-1096	4	1
α-helix	1097-1098	2
β-strand	1099	1	15
α-helix	1109-1110	2
β-strand	1111	1	16
α-helix	1112-1113	2
α-helix	1119	1
β-strand	1120-1121	2	16
α-helix	1128-1131	4
β-strand	1133-1134	2	16
α-helix	1137-1138	2
β-strand	1139-1151	13	17
β-strand	1156-1167	12	17
α-helix	1171-1176	6
α-helix	1178-1184	7
β-strand	1187-1188	2	17
β-strand	1196-1198	3	17
β-strand	1200	1	15
β-strand	1202-1205	4	3
α-helix	1207-1209	3
β-strand	1211-1216	6	3
β-strand	1219-1222	4	3
α-helix	1230-1239	10
α-helix	1249-1261	13
α-helix	1265-1276	12
α-helix	1277-1281	5
α-helix	1284-1296	13
α-helix	1302-1311	10
α-helix	1312-1314	3
β-strand	1319	1	3
β-strand	1324-1325	2	18
β-strand	1330-1331	2	18
α-helix	1332-1333	2
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
CRISPR-associated endonuclease Cas9/Csn1	A	protein	1369	Streptococcus pyogenes	Q99ZW2 (AlphaFold model)
gRNA	B	RNA	98	Streptococcus pyogenes
TS	C	DNA	13	Escherichia phage Lambda
NTS	D	DNA	55	Escherichia phage Lambda
TS	c	DNA	19	Escherichia phage Lambda

Sequence of entity 1 (A), FASTA

>8SRS_1 CRISPR-associated endonuclease Cas9/Csn1 (chains A)
EDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAE
RTRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFG
NIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSD
VDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGN
LIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAI
LLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYA
GYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELH
AILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEE
VVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFL
SGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKI
IKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWG
RLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSL
HEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRER
MKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDH
IVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNL
TKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKS
KLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRK
MIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDF
ATVRKVLSMPQVNIVKKTEVQTGGFSKESIRPKRNSDKLIARKKDWDPKKYGGFLWPTVA
YSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPK
YSLFELENGRKRMLASAKQLQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVE
QHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTRLGA
PRAFKYFDTTIDPKQYRSTKEVLDATLIHQSITGLYETRIDLSQLGGDG

Sequence of entity 2 (B), FASTA

>8SRS_2 gRNA (chains B)
GACGCAUAAAGAUGAGACGCGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUC
CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUU

Sequence of entity 3 (C), FASTA

>8SRS_3 TS (chains C)
TTGTACTGTAGCG

Sequence of entity 4 (D), FASTA

>8SRS_4 NTS (chains D)
AGCAGAAATCTCTGCTGACGCATAAAGATGAGACGCTACAGTACAAACGTCAGCT

Sequence of entity 5 (c), FASTA

>8SRS_5 TS (chains c)
TCTCATCTTTATGCGTCAG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4

Primary citation

Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. Hibshman, G.N., Bravo, J.P.K., Hooper, M.M. et al. Nat Commun (2024) 15:3663-3663. DOI 10.1038/s41467-024-47830-3 · 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 more

8SRS is part of these collections:

CRISPR and genome editing

About this viewer

MolViewer shows 8SRS directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.