5FW1: SpyCas9 variant VQR

Crystal structure of SpyCas9 variant VQR bound to sgRNA and TGAG PAM target DNA. Determined by X-ray diffraction at 2.5 Å resolution. Released 20 Apr 2016.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: SYNTHETIC CONSTRUCT, STREPTOCOCCUS PYOGENES
Chains: 4
Atoms: 13,514
Mol. weight: 198.51 kDa
Ligands: MG
Released: 20 Apr 2016

Explore 5FW1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5FW1 contains 85 α-helices and 55 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: 85 helices, 55 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	108-110	3
α-helix	122-131	10
α-helix	135-144	10
α-helix	151-163	13
β-strand	167	1	4
α-helix	182-195	14
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	287-306	20
α-helix	316-342	27
α-helix	344-346	3
α-helix	347-351	5
α-helix	359-363	5
α-helix	369-381	13
α-helix	387-394	8
α-helix	405-409	5
β-strand	411	1	4
α-helix	412-427	16
α-helix	431-445	15
β-strand	467	1	6
α-helix	472-473	2
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	579-580	2	9
β-strand	584	1	10
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	637-642	6
α-helix	645-653	9
β-strand	659-663	5	8
α-helix	664	1
α-helix	665-669	5
α-helix	679-684	6
α-helix	693-698	6
α-helix	704-709	6
α-helix	720-726	7
α-helix	731-750	20
α-helix	754-756	3
β-strand	758-763	6	1
α-helix	777-791	15
α-helix	795-798	4
α-helix	803-807	5
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
β-strand	855-858	4	12
α-helix	861-864	4
α-helix	872	1
α-helix	873-889	17
α-helix	894-900	7
α-helix	902-905	4
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	1031-1041	11
α-helix	1042-1046	5
β-strand	1063-1065	3	14
β-strand	1072-1075	4	14
α-helix	1079-1088	10
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
α-helix	1119	1
β-strand	1120	1	18
α-helix	1121	1
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	1196-1198	3	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	1254-1261	8
α-helix	1265-1276	12
α-helix	1277-1281	5
α-helix	1284-1296	13
α-helix	1297-1299	3
α-helix	1302-1316	15
β-strand	1319	1	3
β-strand	1324-1325	2	20
β-strand	1330-1331	2	20
β-strand	1336	1	3
α-helix	1340-1344	5
β-strand	1346-1350	5	3
β-strand	1357-1361	5	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sgrna	A	RNA	83	SYNTHETIC CONSTRUCT
CRISPR-associated endonuclease CAS9/CSN1	B	protein	1372	STREPTOCOCCUS PYOGENES	Q99ZW2 (AlphaFold model)
Target DNA strand	C	DNA	28	SYNTHETIC CONSTRUCT
Non-target DNA strand	D	DNA	12	SYNTHETIC CONSTRUCT

Sequence of entity 1 (A), FASTA

>5FW1_1 SGRNA (chains A)
GGAUAACUCAAUUUGUAAAAAAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAG
UCCGUUAUCAACUUGAAAAAGUG

Sequence of entity 2 (B), FASTA

>5FW1_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
GRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFVS
PTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLII
KLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQ
LFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLT
NLGAPAAFKYFDTTIDRKQYRSTKEVLDATLIHQSITGLYETRIDLSQLGGD

Sequence of entity 3 (C), FASTA

>5FW1_3 TARGET DNA STRAND (chains C)
CAATCTCATTTTTTACAAATTGAGTTAT

Sequence of entity 4 (D), FASTA

>5FW1_4 NON-TARGET DNA STRAND (chains D)
AAAATGAGATTG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

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

Primary citation

Structural Plasticity of Pam Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9. Anders, C., Bargsten, K., Jinek, M. Mol Cell (2016) 61:895. DOI 10.1016/J.MOLCEL.2016.02.020 · 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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