6O56: HNH Nuclease from S. pyogenes Cas9

HNH Nuclease from S. pyogenes Cas9. Determined by X-ray diffraction at 1.9 Å resolution. Released 15 Jan 2020.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Streptococcus pyogenes serotype M1
Chains: 2
Atoms: 2,525
Mol. weight: 31.97 kDa
Released: 15 Jan 2020

Explore 6O56 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6O56 contains 22 α-helices and 8 β-strands across 2 chains. 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: 11 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	4-18	15
α-helix	22-25	4
α-helix	30-34	5
α-helix	36-43	8
β-strand	47	1	1
β-strand	54	1	1
α-helix	57-62	6
β-strand	64-67	4	2
α-helix	79-81	3
β-strand	82-85	4	2
α-helix	88-91	4
α-helix	99	1
α-helix	100-115	16
α-helix	121-127	7
α-helix	129-132	4

Chain B: 11 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	2-18	17
α-helix	22-25	4
α-helix	30-34	5
α-helix	36-43	8
β-strand	47	1	3
β-strand	54	1	3
α-helix	60-62	3
β-strand	64-67	4	4
α-helix	79-81	3
β-strand	82-85	4	4
α-helix	88-91	4
α-helix	99	1
α-helix	100-115	16
α-helix	121-127	7
α-helix	129-132	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated endonuclease Cas9/Csn1	A, B	protein	135	Streptococcus pyogenes serotype M1	Q99ZW2 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6O56_1 CRISPR-associated endonuclease Cas9/Csn1 (chains A, B)
SKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRL
SDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLIT
QRKFDNLTKAERGGL

Primary citation

Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics. East, K.W., Newton, J.C., Morzan, U.N. et al. J Am Chem Soc (2020) 142:1348-1358. DOI 10.1021/jacs.9b10521 · 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
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…
7QQS 2.4 Å, SpCas9 bound to FANCF on-target DNA substrate

Browse structure collections

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