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8ygj

SpCas9-MMLV RT-pegRNA-target DNA complex (elongation 28-nt)

Method: ELECTRON MICROSCOPY Dmax: 161.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Gag-Pol polyprotein

Moloney murine leukemia virus

UniProt Q8UN00

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 DNA 3 RNA 1 PDB declaration: hexameric（6） Consistent with all polymer counts Chain E； UniProt 660–1155 Mutation：D200N, D209N, T306K, W313F, T330P, D335N RNA (137-MER) × 1 DNA (51-MER) × 1 ;DNA (5'-D(P*TP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*TP*AP*CP*TP*AP*G)-3') ; × 1 DNA (62-MER) × 1 CRISPR-associated endonuclease Cas9/Csn1 × 1 （Q99ZW2） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.20 Å

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 8YGJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2N3K Human Brd4 ET domain in complex with MLV Integrase C-term Deposited 2015-06-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1719–1735（17 aa） Fragment：MLV integrase C-terminal EBM (UNP residues 1719-1735)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.25；Pressure ambient
NMR sample composition 0.4-0.8 mM [U-99% 13C; U-99% 15N] Brd4 ET, 0.4-0.8 mM MLV IN EBM, 20 mM [U-2H] TRIS, 100 mM sodium chloride, 0.002 v/v sodium azide, 0.5 mM DSS, 2 mM [U-2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4-0.8 mM [U-99% 13C; U-99% 15N] Brd4 ET, 0.4-0.8 mM MLV IN EBM, 20 mM [U-2H] TRIS, 100 mM sodium chloride, 0.002 v/v sodium azide, 0.5 mM DSS, 2 mM [U-2H] DTT, 100% D2O | 100% D2O
NMR sample composition 0.4-0.8 mM [U-99% 15N] Brd4 ET, 0.4-0.8 mM MLV IN EBM, 20 mM [U-2H] TRIS, 100 mM sodium chloride, 0.002 v/v sodium azide, 0.5 mM DSS, 2 mM [U-2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4-0.8 mM [U-99% 15N] Brd4 ET, 20 mM [U-2H] TRIS, 100 mM sodium chloride, 0.002 v/v sodium azide, 0.5 mM DSS, 2 mM [U-2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM MLV IN EBM, 0.5 mM DSS, 0.002 v/v sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7JYZ Solution NMR structure and dynamics of human Brd3 ET in complex with MLV IN CTD Deposited 2020-09-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1659–1738（80 aa） Fragment：C-terminal domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1
NMR sample composition 0.25 mM [U-100% 13C; U-100% 15N] Brd3 ET, 0.25 mM [U-100% 13C; U-100% 15N] MLV-IN-CTD, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.25 mM [U-15N] Brd3 ET, 0.25 mM [U-15N] MLV-IN-CTD, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7UYN Crystal structure of B-form alien DNA 5'-CTTBPPBBSSZZSAAG in a host-guest complex with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase Deposited 2022-05-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 683–937（255 aa） Fragment：N-terminal fragment (UNP residues 683-937)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.05 M ADA, pH 6.5, 9% PEG4000
Resolution 1.65 Å R-free 0.246
7UYO Crystal structure of B-form alien DNA 5'-CTTSSPBZPSZBBAAG in a host-guest complex with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase Deposited 2022-05-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 683–937（255 aa） Fragment：N-terminal fragment (UNP residues 683-937)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.05 M ADA, pH 6.5, 9% PEG4000
Resolution 1.65 Å R-free 0.257
7UYP Crystal structure of B-form alien DNA 5'-CTTZZPBSBSZPPAAG in a host-guest complex with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase Deposited 2022-05-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 683–937（255 aa） Fragment：N-terminal fragment (UNP residues 683-937)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.05 M ADA, pH 6.5, 9% PEG4000
Resolution 1.50 Å R-free 0.234
8CS0 Crystal structure of alien DNA CTSZZPBSBSZPPBAG in a host-guest complex with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase Deposited 2022-05-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 683–937（255 aa） Fragment：N-terminal fragment (UNP residues 683-937)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.05 M ADA, pH 6.5, 9% PEG4000
Resolution 1.65 Å R-free 0.243
8DW1 Crystal structure of a host-guest complex with 5'-CTTAGTTATAACTAAG-3' Deposited 2022-07-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 683–937（255 aa） Fragment：N-terminal fragment (UNP residues 683-937)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；5 mM magnesium acetate, 50 mM ADA, pH 6.5, 9% PEG4000
Resolution 1.85 Å R-free 0.238
8DW8 Host-guest structure of BLMA2 partially bound to 5'-ATTAGTTATAACTAAT-3' Deposited 2022-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 683–937（255 aa） Fragment：N-terminal fragment (UNP residues 683-937)
Not recorded BLM BLEOMYCIN A2 × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Crystals of the host-guest complex were obtained in 5 mM magnesium acetate, 50 mM ADA, pH 6.5, 9% PEG4000. To obtain complexes with BLM, crystals were soaked in well solutions containing 0.1 mM BLM followed by stabilization in 9% PEG4000, 5 mM magnesium acetate, 100 mM HEPES pH 8.0, 20% ethylene glycol, 0.25 mM BLM until unit cell changes correlating with binding of BLM were detected.
Resolution 2.58 Å R-free 0.276
8DWM Host-guest complex of bleomycin A2 fully bound to CTTAGTTATAACTAAG Deposited 2022-08-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 683–937（255 aa） Fragment：N-terminal fragment (UNP residues 683-937)
Not recorded 3CO COBALT (III) ION × 2 BLM BLEOMYCIN A2 × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Crystals of the host-guest complex were grown in 5 mM magnesium acetate, 0.05 M ADA pH 6.5, 9% PEG4000. To obtain complexes with BLM, crystals were soaked in well solutions containing 0.1 mM BLM followed by stabilization in 9% PEG4000, 5 mM magnesium acetate, 100 mM HEPES, pH 8.0, 20% ethylene glycol, 0.25 mM BLM until unit cell changes correlating with binding of BLM were detected.
Resolution 2.99 Å R-free 0.297
8WUS SpCas9-MMLV RT-pegRNA-target DNA complex (termination) Deposited 2023-10-21 Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: hexameric
Chain E 660–1155（496 aa）
Mutation：D200N, D209N, T306K, W313F, T330P, D335N 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 mutation/modification Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: hexameric
Chain E 660–1155（496 aa）
Mutation：D200N, D249N, T306K, W313F, T330P, D335N No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8WUV SpCas9-MMLV RT-pegRNA-target DNA complex (elongation 16-nt) Deposited 2023-10-21 Different mutation/modification Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: hexameric
Chain E 660–1155（496 aa）
Mutation：D200N, D249N, T306K, W313F, T330P, D335N No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8UN00_MLVMO
Isoform —
PDB entities 4
Chains and sequence ranges Author chain E； PDBConstruct 1–496； UniProt 660–1155

CRISPR-associated endonuclease Cas9/Csn1

Streptococcus pyogenes serotype M1

UniProt Q99ZW2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 DNA 3 RNA 1 PDB declaration: hexameric（6） Consistent with all polymer counts Chain A； UniProt 2–1368 Mutation：H10A, H840A RNA (137-MER) × 1 DNA (51-MER) × 1 ;DNA (5'-D(P*TP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*TP*AP*CP*TP*AP*G)-3') ; × 1 Gag-Pol polyprotein × 1 （Q8UN00） DNA (62-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.20 Å

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 8YGJ 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 mutation/modification Different oligomeric state 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 experimental method 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 experimental method 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 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：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 method 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 method 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 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, 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 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, 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 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, 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 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）
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 method 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 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：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 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：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 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：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 method 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 mutation/modification Different oligomeric state 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 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 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 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, 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 experimental method 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 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, 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 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：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 mutation/modification Different oligomeric state 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 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 mutation/modification Different oligomeric state Different experimental method 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 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：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 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）
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 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）
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 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, 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 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, 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 method 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 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 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 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 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 method 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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, 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 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 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 experimental conditions 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 mutation/modification Different oligomeric state Different experimental conditions 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 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 oligomeric state 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）
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 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 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 × 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 method 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 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 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 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 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 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）
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 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 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）
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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 experimental method 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 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）
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 experimental method 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 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）
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 experimental method 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 mutation/modification Different oligomeric state 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 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 mutation/modification Different oligomeric state Different experimental method 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 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）
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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）
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state 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 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
8SCA Rec3 Domain from S. pyogenes Cas9 Deposited 2023-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 497–713（217 aa）
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
8SPQ SpRY-Cas9:gRNA complex targeting TGG PAM DNA Deposited 2023-05-03 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 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 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 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 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 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 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 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 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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
8YNY Structure of Cas9-sgRNA ribonucleoprotein bound to nucleosome Deposited 2024-03-12 Different construct Different mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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）
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 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 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 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 experimental method 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 mutation/modification Different oligomeric state 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 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 mutation/modification Different oligomeric state 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 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 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 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 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 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 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 mutation/modification Different oligomeric state 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 6
Chains and sequence ranges Author chain A； PDBConstruct 1–1367； UniProt 2–1368

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8ygj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ygj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8ygj
Deposition date deposition_date2024-02-26
Structure title titleSpCas9-MMLV RT-pegRNA-target DNA complex (elongation 28-nt)
Keywords keywordsCRISPR-Cas, RNA BINDING PROTEIN-DNA-RNA COMPLEX; RNA BINDING PROTEIN/DNA/RNA
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier49.79 Å
Radius of gyration Rg (electron density) rg_electron50.23 Å
Forward intensity I(0) i01578570000.00
Molecular weight molecular_weight280720.0 kDa
Excluded volume excluded_volume330810 ų
Envelope volume envelope_volume519020 ų
Hydration-shell volume shell_volume88138 ų
Envelope diameter envelope_diameter169.4 Å
Shell Rg shell_rg52.39 Å
Envelope Rg envelope_rg48.92 Å
Shape Rg shape_rg50.25 Å
Total Rg total_rg50.25 Å
Total atoms total_atoms19466
Residues n_residues2017
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax161.4 Å
Rg (real space) rg_real49.85 Å
Rg uncertainty (real space) rg_real_error1.13 Å
I(0) (real space) i0_real1.5790e+09
I(0) uncertainty (real space) i0_real_error2.9270e+07
Rg (reciprocal space) rg_reciprocal49.79 Å
I(0) (reciprocal space) i0_reciprocal1578000000.0000
Solution quality estimate total_estimate0.8555
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary55.5 Å
Skewness Skewness skewness0.373
Kurtosis Kurtosis kurtosis-0.361
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha156000000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.392
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)