5B2S: Streptococcus pyogenes Cas9 EQR variant

Crystal structure of the Streptococcus pyogenes Cas9 EQR variant in complex with sgRNA and target DNA (TGAG PAM). Determined by X-ray diffraction at 2.2 Å resolution. Released 23 Mar 2016.

Method

X-ray diffraction

Resolution

2.2 Å

Organisms

Streptococcus pyogenes, Streptococcus pyogenes serotype M1

Chains

4

Atoms

13,535

Mol. weight

196.96 kDa

Ligands

MG

Released

23 Mar 2016

Explore 5B2S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5B2S contains 82 α-helices and 58 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, 58 β-strands

Molecules and chains

>5B2S_1 Guide RNA (chains A)
GGAAAUUAGGUGCGCUUGGCGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUC
CGUUAUCAACUUGAAAAAGUG

>5B2S_2 CRISPR-associated endonuclease Cas9 (chains B)
GSGHMDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSG
ETAEATRLKRTARRRYTRRKNRILYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERH
PIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNP
DNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNG
LFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNL
SDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSK
NGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHL
GELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPW
NFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRK
PAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIEEFDSVEISGVEDRFNASLGTYHD
LLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRY
TGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQ
GDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKN
SRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDY
DVDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRK
FDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVI
TLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVY
DVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDK
GRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFES
PTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLII
KLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQ
LFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLT
NLGAPAAFKYFDTTIDRKQYRSTKEVLDATLIHQSITGLYETRIDLSQLGGD

>5B2S_3 Target DNA (chains C)
CAATCTCAGCCAAGCGCACCTAATTTCC

>5B2S_4 Non-target DNA, DNA (5'-D(*TP*GP*AP*GP*AP*TP*TP*G)-3') (chains D)
TGAGATTG

Ligands and cofactors

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

Primary citation

Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9. Hirano, S., Nishimasu, H., Ishitani, R. et al. Mol Cell (2016) 61:886-894. DOI 10.1016/j.molcel.2016.02.018 · PubMed

Related structures

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
• 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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