CRISPR-associated endonuclease Cas9/Csn1
Streptococcus pyogenes
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain B； UniProt 497–713 | Not recorded | EDO 1,2-ETHANEDIOL × 5 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Bis-Tris pH 5.5, 0.2 M sodium chloride, 25% PEG3350 | Resolution 1.67 Å R-free 0.209 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 8SCA | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 4CMP Crystal structure of S. pyogenes Cas9 Deposited 2014-01-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–1368（1368 aa）
|
Not recorded | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；0.1 M TRIS PH 8.5, 0.3 M LITHIUM SULFATE, 15% PEG 3350
|
Resolution 2.62 Å R-free 0.286 |
| 4CMP Crystal structure of S. pyogenes Cas9 Deposited 2014-01-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–1368（1368 aa）
|
Not recorded | SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；0.1 M TRIS PH 8.5, 0.3 M LITHIUM SULFATE, 15% PEG 3350
|
Resolution 2.62 Å R-free 0.286 |
| 4CMQ Crystal structure of Mn-bound S.pyogenes Cas9 Deposited 2014-01-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–1368（1368 aa）
|
Not recorded | MN MANGANESE (II) ION × 7 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；0.1 M TRIS 8.5, 0.3 M LITHIUM SULFATE, 15% PEG 3350 SOAKED IN MOTHER LIQUOR SUPPLEMENTED WITH 20 MM MNCL2
|
Resolution 3.09 Å R-free 0.277 |
| 4CMQ Crystal structure of Mn-bound S.pyogenes Cas9 Deposited 2014-01-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–1368（1368 aa）
|
Not recorded | MN MANGANESE (II) ION × 6 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；0.1 M TRIS 8.5, 0.3 M LITHIUM SULFATE, 15% PEG 3350 SOAKED IN MOTHER LIQUOR SUPPLEMENTED WITH 20 MM MNCL2
|
Resolution 3.09 Å R-free 0.277 |
| 4OO8 Crystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNA Deposited 2014-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–1368（1368 aa）
|
Mutation：D10A/C80L/H840A/C574E | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；12% PEG 3350, 100mM Tris-HCl, 200mM ammonium acetate, 150mM NaCl, 100mM NDSB-256, pH 8.0, vapor diffusion, hanging drop, temperature 293K
|
Resolution 2.50 Å R-free 0.254 |
| 4OO8 Crystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNA Deposited 2014-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: trimeric |
Chain D
1–1368（1368 aa）
|
Mutation：D10A/C80L/H840A/C574E | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；12% PEG 3350, 100mM Tris-HCl, 200mM ammonium acetate, 150mM NaCl, 100mM NDSB-256, pH 8.0, vapor diffusion, hanging drop, temperature 293K
|
Resolution 2.50 Å R-free 0.254 |
| 4UN3 Crystal structure of Cas9 bound to PAM-containing DNA target Deposited 2014-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：YES | MG MAGNESIUM ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；0.1 M TRIS-ACETATE PH 8.5, 0.3 M KSCN, 15% (W/V) PEG 3350
|
Resolution 2.59 Å R-free 0.252 |
| 4UN4 Crystal structure of Cas9 bound to PAM-containing DNA target with mismatches at positions 1-2 Deposited 2014-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain B
1–1368（1368 aa）
|
Mutation：YES | MG MAGNESIUM ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；0.1 M TRIS-ACETATE, PH 8.5, 0.3 M KSCN, 15% (W/V) PEG 3350
|
Resolution 2.37 Å R-free 0.248 |
| 4UN5 Crystal structure of Cas9 bound to PAM-containing DNA target containing mismatches at positions 1-3 Deposited 2014-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain B
1–1368（1368 aa）
|
Mutation：YES | MG MAGNESIUM ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；0.1 M TRIS-ACETATE PH 8.5, 0.3 M KSCN, 15% PEG (W/V) 3350
|
Resolution 2.40 Å R-free 0.246 |
| 5B2R Crystal structure of the Streptococcus pyogenes Cas9 VQR variant in complex with sgRNA and target DNA (TGA PAM) Deposited 2016-02-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, C80L, C574E, H840A, D1135V, R1335Q, T1337R | K POTASSIUM ION × 11 MG MAGNESIUM ION × 3 EDO 1,2-ETHANEDIOL × 4 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；15-17% PEG 3350, 0.4 M KSCN, 0.1 M Tris-acetate
|
Resolution 2.00 Å R-free 0.230 |
| 5B2S Crystal structure of the Streptococcus pyogenes Cas9 EQR variant in complex with sgRNA and target DNA (TGAG PAM) Deposited 2016-02-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, C80L, C574E, H840A, D1135E, R1335Q, T1337R | K POTASSIUM ION × 11 MG MAGNESIUM ION × 3 EDO 1,2-ETHANEDIOL × 4 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；15-17% PEG 3350, 0.4 M KSCN, 0.1 M Tris-acetate
|
Resolution 2.20 Å R-free 0.231 |
| 5B2T Crystal structure of the Streptococcus pyogenes Cas9 VRER variant in complex with sgRNA and target DNA (TGCG PAM) Deposited 2016-02-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, C80L, C574E, H840A, D1135V, G1218R, R1335E, T1337R | K POTASSIUM ION × 10 MG MAGNESIUM ION × 3 EDO 1,2-ETHANEDIOL × 5 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；15-17% PEG 3350, 0.4 M KSCN, 0.1 M Tris-acetate
|
Resolution 2.20 Å R-free 0.223 |
| 5F9R Crystal structure of catalytically-active Streptococcus pyogenes CRISPR-Cas9 in complex with single-guided RNA and double-stranded DNA primed for target DNA cleavage Deposited 2015-12-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Not recorded | SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.8 M ammonium sulfate, 100 mM Tris-HCl pH8.0 and 10 mM EDTA
|
Resolution 3.40 Å R-free 0.299 |
| 5FQ5 Crystal structure of Cas9-sgRNA-DNA complex solved by native SAD phasing Deposited 2015-12-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain B
1–1368（1368 aa）
|
Mutation：YES | MG MAGNESIUM ION × 2 K POTASSIUM ION × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；0.1 M TRIS-ACETATE PH 8.5, 0.3 M KSCN, 15% PEG (W/V) 3350
|
Resolution 2.14 Å R-free 0.225 |
| 5FW1 Crystal structure of SpyCas9 variant VQR bound to sgRNA and TGAG PAM target DNA Deposited 2016-02-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：YES | K POTASSIUM ION × 13 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；0.1 M TRIS PH 8.5, 0.3 M KSCN, 15% (W/V) PEG 3400
|
Resolution 2.50 Å R-free 0.254 |
| 5FW2 Crystal structure of SpCas9 variant EQR bound to sgRNA and TGAG PAM target DNA Deposited 2016-02-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：YES | MG MAGNESIUM ION × 2 K POTASSIUM ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；0.1 M TRIS PH 8.5 0.3M KSCN 15% (W/V) PEG 3400
|
Resolution 2.68 Å R-free 0.231 |
| 5FW3 Crystal structure of SpCas9 variant VRER bound to sgRNA and TGCG PAM target DNA Deposited 2016-02-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：YES | MG MAGNESIUM ION × 2 K POTASSIUM ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；0.1 M TRIS PH 8.5 0.3M KSCN 15% (W/V) PEG 3400
|
Resolution 2.70 Å R-free 0.242 |
| 5VW1 Crystal structure of SpyCas9-sgRNA-AcrIIA4 ternary complex Deposited 2017-05-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain A
1–1368（1368 aa）
|
Mutation：D10A/H840A | PEG DI(HYDROXYETHYL)ETHER × 2 PG4 TETRAETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7.2；293 K；0.1 M HEPES (pH 7.5), and 15% PEG3350 (v/v)
|
Resolution 2.60 Å R-free 0.226 |
| 5XBL Structure of nuclease in complex with associated protein Deposited 2017-03-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris-HCl, pH 6.5, 0.2 M MgCl2 and 14% (w/v) Polyethylene glycol (PEG) 4000
|
Resolution 3.05 Å R-free 0.277 |
| 5Y36 Cryo-EM structure of SpCas9-sgRNA-DNA ternary complex Deposited 2017-07-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20mM Tris-Cl (pH 7.5), 100mM KCl, 5mM MgCl2, 1mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 4 seconds before pluging
|
Resolution 5.20 Å |
| 6AEB Crystal structure of xCas9 in complex with sgRNA and target DNA (AAG PAM) Deposited 2018-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, A263T, R324L, S409I, E480K, E543D, M694I, H840A, E1219V | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Hepes, PH 7.5, 0.2M Ammonium sulfate, 10% ispropanol, and 16% (w/v) PEG4000
|
Resolution 3.00 Å R-free 0.283 |
| 6AEB Crystal structure of xCas9 in complex with sgRNA and target DNA (AAG PAM) Deposited 2018-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain F
1–1368（1368 aa）
|
Mutation：D10A, A263T, R324L, S409I, E480K, E543D, M694I, H840A, E1219V | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Hepes, PH 7.5, 0.2M Ammonium sulfate, 10% ispropanol, and 16% (w/v) PEG4000
|
Resolution 3.00 Å R-free 0.283 |
| 6AEG Crystal structure of xCas9 in complex with sgRNA and target DNA (GAT PAM) Deposited 2018-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, A263T, R324L, S409I, E480K, E543D, M694I, H840A, E1219V | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Hepes, pH 7.5, 0.2M Ammonium sulfate, 10% ispropanol, 16% (w/v) PEG4000, 30%(v/v) (+/-)-2-Methyl-2,4-pentanediol
|
Resolution 2.70 Å R-free 0.263 |
| 6AI6 Crystal structure of SpCas9-NG Deposited 2018-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Mutation：N863A, L1111R, D1135V, G1218R, E1219F, A1322R, R1355V, T1357R | K POTASSIUM ION × 10 MG MAGNESIUM ION × 3 EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Tris-acetate, pH 8.0, KSCN, PEG 3350
|
Resolution 2.70 Å R-free 0.243 |
| 6IFO Crystal structure of AcrIIA2-SpyCas9-sgRNA ternary complex Deposited 2018-09-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；0.1 M Bis-Tris, pH 6.0, 15% PEG 20000
|
Resolution 3.31 Å R-free 0.268 |
| 6IFO Crystal structure of AcrIIA2-SpyCas9-sgRNA ternary complex Deposited 2018-09-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain B
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；0.1 M Bis-Tris, pH 6.0, 15% PEG 20000
|
Resolution 3.31 Å R-free 0.268 |
| 6K3Z Crystal structure of dCas9 in complex with sgRNA and DNA (TGA PAM) Deposited 2019-05-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：H840A, D10A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；0.2M Ammonium phosphate dibasic, 20%(w/v) Polyethylene glycol 3,350
|
Resolution 3.20 Å R-free 0.276 |
| 6K4P Crystal structure of xCas9 in complex with sgRNA and DNA (TGG PAM) Deposited 2019-05-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Not recorded | PO4 PHOSPHATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；0.2M Ammonium phosphate dibasic, 20%(w/v) Polyethylene glycol 3,350
|
Resolution 2.90 Å R-free 0.269 |
| 6K4Q Crystal structure of xCas9 in complex with sgRNA and DNA (CGG PAM) Deposited 2019-05-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Not recorded | PO4 PHOSPHATE ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；0.2M Ammonium phosphate dibasic, 20%(w/v) Polyethylene glycol 3,350
|
Resolution 2.70 Å R-free 0.275 |
| 6K4S Crystal structure of xCas9 in complex with sgRNA and DNA (TGC PAM) Deposited 2019-05-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, C80L, A262T, R324L, S409T, E480K, E543D, C574E, M694I, H840A, E1219V | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；0.2 M Ammonium phosphate dibasic, 20% w/v Polyethylene glycol 3,350
|
Resolution 3.01 Å R-free 0.285 |
| 6K4U Crystal structure of xCas9 in complex with sgRNA and DNA (TGA PAM) Deposited 2019-05-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, A262T, R324L, S409T, E480K, E543D, M694I, H840A, E1219V | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；0.2 M Ammonium phosphate dibasic, 20% w/v Polyethylene glycol 3,350
|
Resolution 3.20 Å R-free 0.282 |
| 6K57 Crystal structure of dCas9 in complex with sgRNA and DNA (CGA PAM) Deposited 2019-05-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；0.2M Ammonium phosphate dibasic, 20%(w/v) Polyethylene glycol 3,350
|
Resolution 2.98 Å R-free 0.274 |
| 6O0X Conformational states of Cas9-sgRNA-DNA ternary complex in the presence of magnesium Deposited 2019-02-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.28 Å |
| 6O0Y Conformational states of Cas9-sgRNA-DNA ternary complex in the presence of magnesium Deposited 2019-02-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.37 Å |
| 6O0Z Conformational states of Cas9-sgRNA-DNA ternary complex in the presence of magnesium Deposited 2019-02-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 6O56 HNH Nuclease from S. pyogenes Cas9 Deposited 2019-03-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
775–908（134 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M [imidazole and MES] pH 6.5, 25% (v/v) [2-methyl-2,4-pentanediol, PEG1000, and PEG3350], 0.3 M [diethylene glycol, triethylene glycol, tetraethylene glycol, pentaethlyene glycol]
|
Resolution 1.90 Å R-free 0.253 |
| 6O56 HNH Nuclease from S. pyogenes Cas9 Deposited 2019-03-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
775–908（134 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M [imidazole and MES] pH 6.5, 25% (v/v) [2-methyl-2,4-pentanediol, PEG1000, and PEG3350], 0.3 M [diethylene glycol, triethylene glycol, tetraethylene glycol, pentaethlyene glycol]
|
Resolution 1.90 Å R-free 0.253 |
| 7OX7 Target-bound SpCas9 complex with TRAC chimeric RNA-DNA guide Deposited 2021-06-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 2.60 Å R-free 0.229 |
| 7OX8 Target-bound SpCas9 complex with TRAC full RNA guide Deposited 2021-06-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 2.75 Å R-free 0.248 |
| 7OX9 Target-bound SpCas9 complex with AAVS1 all-RNA guide Deposited 2021-06-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 2.45 Å R-free 0.233 |
| 7OXA Target-bound SpCas9 complex with AAVS1 chimeric RNA-DNA guide Deposited 2021-06-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 2.15 Å R-free 0.226 |
| 7QQO SpCas9 bound to AAVS1 off-target1 DNA substrate Deposited 2022-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 3.00 Å R-free 0.247 |
| 7QQP SpCas9 bound to AAVS1 off-target3 DNA substrate Deposited 2022-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 10 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 2.60 Å R-free 0.225 |
| 7QQQ SpCas9 bound to AAVS1 off-target4 DNA substrate Deposited 2022-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 13 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 2.65 Å R-free 0.235 |
| 7QQR SpCas9 bound to AAVS1 off-target5 DNA substrate Deposited 2022-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 13 EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 2.75 Å R-free 0.231 |
| 7QQS SpCas9 bound to FANCF on-target DNA substrate Deposited 2022-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 2.40 Å R-free 0.229 |
| 7QQT SpCas9 bound to FANCF off-target1 DNA substrate Deposited 2022-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 2.50 Å R-free 0.238 |
| 7QQU SpCas9 bound to FANCF off-target2 DNA substrate Deposited 2022-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 2.45 Å R-free 0.231 |
| 7QQV SpCas9 bound to FANCF off-target3 DNA substrate Deposited 2022-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 2.25 Å R-free 0.230 |
| 7QQW SpCas9 bound to FANCF off-target4 DNA substrate Deposited 2022-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 3.10 Å R-free 0.234 |
| 7QQX SpCas9 bound to FANCF off-target5 DNA substrate Deposited 2022-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 2.40 Å R-free 0.216 |
| 7QQZ SpCas9 bound to FANCF off-target7 DNA substrate Deposited 2022-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 2.25 Å R-free 0.247 |
| 7QR0 SpCas9 bound to TRAC off-target1 DNA substrate Deposited 2022-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 17 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 2.30 Å R-free 0.224 |
| 7QR1 SpCas9 bound to TRAC off-target2 DNA substrate Deposited 2022-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 2.60 Å R-free 0.231 |
| 7QR5 SpCas9 bound to FANCF off-target6 DNA substrate Deposited 2022-01-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 11 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 3.30 Å R-free 0.254 |
| 7QR7 SpCas9 bound to AAVS1 off-target2 DNA substrate Deposited 2022-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 3.00 Å R-free 0.245 |
| 7QR8 SpCas9 bound to PTPRC off-target1 DNA substrate Deposited 2022-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 2.75 Å R-free 0.250 |
| 7S36 Cas9:sgRNA:DNA (S. pyogenes) with 0 RNA:DNA base pairs, closed-protein/bent-DNA conformation Deposited 2021-09-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain P
1–1368（1368 aa）
|
Mutation：T1337C | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7S37 Cas9:sgRNA (S. pyogenes) in the open-protein conformation Deposited 2021-09-04 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain P
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7S38 Cas9:sgRNA:DNA (S. pyogenes) forming a 3-base-pair R-loop Deposited 2021-09-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain P
1–1368（1368 aa）
|
Mutation：T1337C | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7S3H Cas9:sgRNA:DNA (S. pyogenes) with 0 RNA:DNA base pairs, open-protein/linear-DNA conformation Deposited 2021-09-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain P
1–1368（1368 aa）
|
Mutation：T1337C | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 7S4U Cryo-EM structure of Cas9 in complex with 12-14MM DNA substrate, 5 minute time-point Deposited 2021-09-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.56 Å |
| 7S4V Cas9 bound to 12-14MM DNA, 60 min time-point, kinked conformation Deposited 2021-09-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.28 Å |
| 7S4X Cas9:gRNA in complex with 18-20MM DNA, 1 minute time-point, kinked active conformation Deposited 2021-09-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
1–1368（1368 aa）
|
Not recorded | MG MAGNESIUM ION × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.76 Å |
| 7V59 Cryo-EM structure of spyCas9-sgRNA-DNA dimer Deposited 2021-08-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: hexameric |
Chain B
3–1364（1362 aa）
Chain E
3–1364（1362 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.26 Å |
| 7VK9 Crystal structure of xCas9 P411T Deposited 2021-09-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–1368（1368 aa）
|
Mutation：P411T,R324L,S409I,E480K,A262T,E543D,M694I,E1219V | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1M Sodium Cacodylate pH 7.0, 1M Sodium citrate tribasic dehydrate
|
Resolution 2.90 Å R-free 0.234 |
| 7Z4C SpCas9 bound to 6 nucleotide complementary DNA substrate Deposited 2022-03-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10, H840 | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.87 Å |
| 7Z4D Crystal structure of SpCas9 bound to a 10 nucleotide complementary DNA substrate Deposited 2022-03-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | K POTASSIUM ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；0.1 M sodium cacodylate pH 6.5, 0.8-1.2M ammonium formate, 12-14% PEG4000
|
Resolution 3.10 Å R-free 0.276 |
| 7Z4D Crystal structure of SpCas9 bound to a 10 nucleotide complementary DNA substrate Deposited 2022-03-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain E
1–1368（1368 aa）
|
Mutation：D10A, H840A | K POTASSIUM ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；0.1 M sodium cacodylate pH 6.5, 0.8-1.2M ammonium formate, 12-14% PEG4000
|
Resolution 3.10 Å R-free 0.276 |
| 7Z4E SpCas9 bound to 8-nucleotide complementary DNA substrate Deposited 2022-03-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 4.14 Å |
| 7Z4G SpCas9 bound to 12-nucleotide complementary DNA substrate Deposited 2022-03-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.64 Å |
| 7Z4H SpCas9 bound to 14-nucleotide complementary DNA substrate Deposited 2022-03-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.49 Å |
| 7Z4I SpCas9 bound to 16-nucleotide complementary DNA substrate Deposited 2022-03-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | K POTASSIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.12 Å |
| 7Z4J SpCas9 bound to 18-nucleotide complementary DNA substrate in the catalytic state Deposited 2022-03-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain B
1–1368（1368 aa）
|
Not recorded | MG MAGNESIUM ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.99 Å |
| 7Z4K SpCas9 bound to 10-nucleotide complementary DNA substrate Deposited 2022-03-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.81 Å |
| 7Z4L SpCas9 bound to 18-nucleotide complementary DNA substrate in the checkpoint state Deposited 2022-03-04 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Not recorded | MG MAGNESIUM ION × 1 K POTASSIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.54 Å |
| 7ZO1 SpCas9 bound to CD34 off-target9 DNA substrate Deposited 2022-04-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Mutation：D10A, H840A | MG MAGNESIUM ION × 2 K POTASSIUM ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350
|
Resolution 2.40 Å R-free 0.250 |
| 8FZT SpCas9 with dual-guide RNA and target DNA Deposited 2023-01-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain E
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.03 Å |
| 8G1I SpCas9 with sgRNA and target DNA Deposited 2023-02-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.12 Å |
| 8KAG Crystal structure of SpyCas9 in complex with sgRNA and target RNA Deposited 2023-08-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain B
1–1368（1368 aa）
|
Mutation：A10D,A840H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；1.7 M Ammonium citrate tribasic, 0.1 M HEPES pH 7.0
|
Resolution 3.88 Å R-free 0.320 |
| 8KAH Crystal structure of SpyCas9-crRNA-tracrRNA complex bound to 18nt target DNA Deposited 2023-08-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain B
1–1368（1368 aa）
|
Mutation：A10D,A840H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；1.0 M Sodium chloride, 0.1 M Sodium citrate pH 6.0, 13.25% PEG4000
|
Resolution 3.36 Å R-free 0.255 |
| 8KAH Crystal structure of SpyCas9-crRNA-tracrRNA complex bound to 18nt target DNA Deposited 2023-08-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain F
1–1368（1368 aa）
|
Mutation：A10D,A840H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；1.0 M Sodium chloride, 0.1 M Sodium citrate pH 6.0, 13.25% PEG4000
|
Resolution 3.36 Å R-free 0.255 |
| 8KAI Crystal structure of SpyCas9-crRNA-tracrRNA complex bound to 17nt target DNA Deposited 2023-08-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain B
1–1368（1368 aa）
|
Mutation：A10D,A840H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；1.0 M Sodium chloride, 0.1 M Sodium citrate pH 6.0, 13% PEG4000
|
Resolution 3.49 Å R-free 0.294 |
| 8KAI Crystal structure of SpyCas9-crRNA-tracrRNA complex bound to 17nt target DNA Deposited 2023-08-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain F
1–1368（1368 aa）
|
Mutation：A10D,A840H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；1.0 M Sodium chloride, 0.1 M Sodium citrate pH 6.0, 13% PEG4000
|
Resolution 3.49 Å R-free 0.294 |
| 8KAJ Crystal structure of SpyCas9-crRNA-tracrRNA complex bound to 16nt target DNA Deposited 2023-08-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain B
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；1.0 M Sodium chloride, 0.1 M Sodium citrate pH 6.0, 12.75% PEG4000
|
Resolution 3.42 Å R-free 0.246 |
| 8KAJ Crystal structure of SpyCas9-crRNA-tracrRNA complex bound to 16nt target DNA Deposited 2023-08-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain F
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；1.0 M Sodium chloride, 0.1 M Sodium citrate pH 6.0, 12.75% PEG4000
|
Resolution 3.42 Å R-free 0.246 |
| 8KAK Crystal structure of SpyCas9 in complex with sgRNA and 18nt target DNA Deposited 2023-08-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.15 M Ammonium sulfate, 0.1 M MES pH 6.0, 14.75% PEG4000
|
Resolution 3.60 Å R-free 0.297 |
| 8KAK Crystal structure of SpyCas9 in complex with sgRNA and 18nt target DNA Deposited 2023-08-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain F
1–1368（1368 aa）
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.15 M Ammonium sulfate, 0.1 M MES pH 6.0, 14.75% PEG4000
|
Resolution 3.60 Å R-free 0.297 |
| 8KAL Crystal structure of SpyCas9 in complex with sgRNA and 17nt target DNA Deposited 2023-08-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.2 M Ammonium sulfate, 0.1 M MES pH 6.0, 12.625% PEG8000
|
Resolution 3.16 Å R-free 0.288 |
| 8KAL Crystal structure of SpyCas9 in complex with sgRNA and 17nt target DNA Deposited 2023-08-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain G
1–1368（1368 aa）
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.2 M Ammonium sulfate, 0.1 M MES pH 6.0, 12.625% PEG8000
|
Resolution 3.16 Å R-free 0.288 |
| 8KAM Crystal structure of SpyCas9 in complex with sgRNA and 16nt target DNA Deposited 2023-08-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.15 M Ammonium sulfate, 0.1 M MES pH 6.0, 14.75% PEG4000
|
Resolution 3.91 Å R-free 0.290 |
| 8SPQ SpRY-Cas9:gRNA complex targeting TGG PAM DNA Deposited 2023-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
2–1368（1367 aa）
|
Mutation：A61R,L1111R,D1135L,S1136W,G1218K,E1219Q,N1317R,A1322R R1333P,R1335Q,T1337R | MG MAGNESIUM ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.26 Å |
| 8SQH SpRY-Cas9:gRNA complex targeting TTC PAM DNA Deposited 2023-05-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
2–1368（1367 aa）
|
Mutation：A61R, L1111R, D1135L, S1136W, G1218K, E1219Q, N1317R, A1322R, R1333P, R1335Q, T1337R | MG MAGNESIUM ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.69 Å |
| 8SRS SpRY-Cas9:gRNA complex targeting TAC PAM DNA Deposited 2023-05-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
2–1368（1367 aa）
|
Mutation：A61R,L1111R,D1135L,S1136W,G1218K,E1219Q,N1317R,A1322R R1333P,R1335Q,T1337R | MG MAGNESIUM ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.79 Å |
| 8T6O SpRY-Cas9:gRNA complex targeting TAC PAM DNA with 0 bp R-loop Deposited 2023-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
2–1368（1367 aa）
|
Mutation：A61R,L1111R,D1135L,S1136W,G1218K,E1219Q,N1317R,A1322R R1333P,R1335Q,T1337R | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8T6P SpRY-Cas9:gRNA complex targeting TAC PAM DNA with 2 bp R-loop Deposited 2023-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
2–1368（1367 aa）
|
Mutation：A61R, L1111R, D1135L, S1136W, G1218K, E1219Q, N1317R, A1322R, R1333P, R1335Q, T1337R | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.15 Å |
| 8T6S SpRY-Cas9:gRNA complex targeting TAC PAM DNA with 10 bp R-loop Deposited 2023-06-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
2–1368（1367 aa）
|
Mutation：A61R, L1111R, D1135L, S1136W, G1218K, E1219Q, N1317R, A1322R, R1333P, R1335Q, T1337R | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.28 Å |
| 8T6T SpRY-Cas9:gRNA complex targeting TAC PAM DNA with 13 bp R-loop Deposited 2023-06-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
2–1368（1367 aa）
|
Mutation：A61R, L1111R, D1135L, S1136W, G1218K, E1219Q, N1317R, A1322R, R1333P, R1335Q, T1337R | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 8T6X SpRY-Cas9:gRNA complex targeting TAC PAM DNA with 18 bp R-loop Deposited 2023-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
2–1368（1367 aa）
|
Mutation：A61R, L1111R, D1135L, S1136W, G1218K, E1219Q, N1317R, A1322R, R1333P, R1335Q, T1337R | MG MAGNESIUM ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.08 Å |
| 8T6Y SpRY-Cas9:gRNA complex bound to non-target DNA with 1 bp R-loop Deposited 2023-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
2–1368（1367 aa）
|
Mutation：A61R, L1111R, D1135L, S1136W, G1218K, E1219Q, N1317R, A1322R, R1333P, R1335Q, T1337R | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.88 Å |
| 8T76 SpRY-Cas9:gRNA complex targeting TAC PAM DNA with 3 bp R-loop Deposited 2023-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
2–1368（1367 aa）
|
Mutation：A61R, L1111R, D1135L, S1136W, G1218K, E1219Q, N1317R, A1322R, R1333P, R1335Q, T1337R | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 8T77 SpRY-Cas9:gRNA complex bound to non-target DNA with 6 bp R-loop Deposited 2023-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
2–1368（1367 aa）
|
Mutation：A61R, L1111R, D1135L, S1136W, G1218K, E1219Q, N1317R, A1322R, R1333P, R1335Q, T1337R | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.25 Å |
| 8T78 SpRY-Cas9:gRNA complex bound to non-target DNA with 8 bp R-loop Deposited 2023-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
2–1368（1367 aa）
|
Mutation：A61R, L1111R, D1135L, S1136W, G1218K, E1219Q, N1317R, A1322R, R1333P, R1335Q, T1337R | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.02 Å |
| 8T79 SpRY-Cas9:gRNA complex bound to non-target DNA with 10 bp R-loop Deposited 2023-06-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
3–1366（1364 aa）
|
Mutation：A61R, L1111R, D1135L, S1136W, G1218K, E1219Q, N1317R, A1322R, R1333P, R1335Q, T1337R | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 8T7S SpRYmer bound to NAC PAM DNA Deposited 2023-06-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: heptameric |
Chain A
2–1368（1367 aa）
Chain G
2–1368（1367 aa）
|
Mutation：A61R, L1111R, D1135L, S1136W, G1218K, E1219Q, N1317R, A1322R, R1333P, R1335Q, T1337R Mutation：A61R, L1111R, D1135L, S1136W, G1218K, E1219Q, N1317R, A1322R, R1333P, R1335Q, T1337R | MG MAGNESIUM ION × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.01 Å |
| 8TZZ SpG Cas9 with NGC PAM DNA target Deposited 2023-08-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
2–1367（1366 aa）
|
Not recorded | MG MAGNESIUM ION × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.56 Å |
| 8U3Y SpG Cas9 with NGG PAM DNA target Deposited 2023-09-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
3–1366（1364 aa）
|
Not recorded | MG MAGNESIUM ION × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8WUS SpCas9-MMLV RT-pegRNA-target DNA complex (termination) Deposited 2023-10-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: hexameric |
Chain A
2–1368（1367 aa）
|
Mutation：H10A, H840A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8WUT SpCas9-MMLV RT-pegRNA-target DNA complex (initiation) Deposited 2023-10-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: hexameric |
Chain A
2–1368（1367 aa）
|
Mutation：D10A, H840A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8WUU SpCas9-pegRNA-target DNA complex (pre-initiation) Deposited 2023-10-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
2–1368（1367 aa）
|
Mutation：D10A, H840A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8WUV SpCas9-MMLV RT-pegRNA-target DNA complex (elongation 16-nt) Deposited 2023-10-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: hexameric |
Chain A
2–1368（1367 aa）
|
Mutation：D10A, H840A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8YE6 Cryo-EM structure of Cas9-sgRNA-A32 complex Deposited 2024-02-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.95 Å |
| 8YE9 Cryo-EM structure of Cas9-sgRNA-A25 complex Deposited 2024-02-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 3.43 Å |
| 8YGJ SpCas9-MMLV RT-pegRNA-target DNA complex (elongation 28-nt) Deposited 2024-02-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: hexameric |
Chain A
2–1368（1367 aa）
|
Mutation：H10A, H840A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8YNY Structure of Cas9-sgRNA ribonucleoprotein bound to nucleosome Deposited 2024-03-12 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: 13-meric |
Chain X
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.52 Å |
| 9B2K SpCas9 with dual-guide RNA in open conformation Deposited 2024-03-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain P
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.67 Å |
| 9C9P Cas9 ternary complex, 14-nt sgRNA, State I (linear) Deposited 2024-06-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9CGU Cas9 ternary complex, 14-nt sgRNA, State II (kinked) Deposited 2024-07-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9EAK SpCas9 with 17-bp R-loop containing 2 terminal mismatches (State I - pre-activation) Deposited 2024-11-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Not recorded | MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.76 Å |
| 9EAL SpCas9 with 17-bp R-loop containing 2 terminal mismatches (State II - precleavage) Deposited 2024-11-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.83 Å |
| 9ED9 SpCas9 with 17-bp R-loop containing 2 terminal mismatches (State III - checkpoint) Deposited 2024-11-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.95 Å |
| 9EDA SpCas9 with 17-bp R-loop containing 2 terminal mismatches (State IV - product) Deposited 2024-11-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.88 Å |
| 9EDB SpCas9 with 17-bp R-loop containing 2 terminal mismatches (State V - dissociated) Deposited 2024-11-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9H4J dCas9 bound to on-target EMX1-1 (-)SC DNA minicircle Deposited 2024-10-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9H4K dCas9 bound to off-target 1 EMX1-1 (-)SC DNA minicircle Deposited 2024-10-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 9H4L dCas9 bound to off-target 2 EMX1-1 (-)SC DNA minicircle Deposited 2024-10-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
2–1366（1365 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 9H4M wtCas9 bound to off-target 1 EMX1-1 (-)SC DNA minicircle Deposited 2024-10-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 9JL1 SpCas9 with mini-gRNA conformation Deposited 2024-09-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9JL2 Classical conformation for the spCas9 with gRNA and target DNA complex Deposited 2024-09-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9JL4 Apo-spCas9 conformation Deposited 2024-09-17 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 9K4C SuperFi Cas9 - 22nt sgRNA - DNA ternary complex Deposited 2024-10-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Mutation：Y1010D, Y1013D, Y1016D, V1018D, R1019D, Q1027D, K1031D | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.84 Å |
| 9K4D SuperFi Cas9 - 20nt sgRNA - DNA ternary complex Deposited 2024-10-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Mutation：Y1010D, Y1013D, Y1016D, V1018D, R1019D, Q1027D, K1031D | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.53 Å |
| 9K4E SuperFi Cas9 - mismatch 22nt sgRNA - DNA ternary complex class1 Deposited 2024-10-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Mutation：Y1010D, Y1013D, Y1016D, V1018D, R1019D, Q1027D, K1031D | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9K4F SuperFi Cas9 - mismatch 22nt sgRNA - DNA ternary complex class2 Deposited 2024-10-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Mutation：Y1010D, Y1013D, Y1016D, V1018D, R1019D, Q1027D, K1031D | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.27 Å |
| 9K4H SuperFi Cas9 - mismatch 22nt sgRNA - DNA ternary complex class3 Deposited 2024-10-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Mutation：Y1010D, Y1013D, Y1016D, V1018D, R1019D, Q1027D, K1031D | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.36 Å |
| 9KJ6 Crystal Structure of SpCas9 ternary complex, amino acids (1242-1263) replaced with Gly-Ser linker Deposited 2024-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1241（1241 aa）
Chain A
1264–1368（105 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.15 K；0.07 M HEPES (pH 7.5), 0.18 M potassium acetate, 14% (v/v) PEG 3350
|
Resolution 3.59 Å R-free 0.271 |
| 9LKJ Structure of Cas9-sgRNA-A27 Deposited 2025-01-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain C
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.68 Å |
| 9W7Q SuperFi Cas9 - 20nt sgRNA - DNA ternary complex Class A Deposited 2025-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Mutation：Y1010D, Y1013D, Y1016D, V1018D, R1019D, Q1027D, K1031D | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.79 Å |
| 9W7T SuperFi Cas9 - 20nt sgRNA - DNA ternary complex Class B Deposited 2025-08-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.91 Å |
| 9W7U SuperFi Cas9 - 20nt sgRNA - DNA ternary complex Class C Deposited 2025-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Mutation：Y1010D, Y1013D, Y1016D, V1018D, R1019D, Q1027D, K1031D | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.83 Å |
| 9W7V SuperFi Cas9 - 20nt sgRNA - DNA ternary complex Class D Deposited 2025-08-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Mutation：Y1010D, Y1013D, Y1016D, V1018D, R1019D, Q1027D, K1031D | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.81 Å |
| 9W9D SuperFi Cas9 - 22nt sgRNA - DNA ternary complex Deposited 2025-08-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Mutation：Y1010D, Y1013D, Y1016D, V1018D, R1019D, Q1027D, K1031D | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 9WA9 SuperFi Cas9 - 22nt sgRNA - DNA ternary complex Class B Deposited 2025-08-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Mutation：Y1010D, Y1013D, Y1016D, V1018D, R1019D, Q1027D, K1031D | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.12 Å |
| 9WAA SuperFi Cas9 - 22nt sgRNA - DNA ternary complex Class C Deposited 2025-08-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Mutation：Y1010D, Y1013D, Y1016D, V1018D, R1019D, Q1027D, K1031D | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.17 Å |
| 9WAW SuperFi Cas9 - 20nt sgRNA - DNA ternary complex Class E Deposited 2025-08-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–1368（1368 aa）
|
Mutation：Y1010D, Y1013D, Y1016D, V1018D, R1019D, Q1027D, K1031D | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.95 Å |
| 9ZQ6 Structure of SpyCas9 in complex with the anti-CRISPR protein AcrIIA26 Deposited 2025-12-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric |
Chain A
1–1368（1368 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
134 other PDB entries and 146 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | CAS9_STRP1 |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain B； PDBConstruct 2–218； UniProt 497–713 |
