10vc

Crystal structure of GeoCas9 HNH domain bound to anti-CRISPR AcrIIC1

Method: X-RAY DIFFRACTION Dmax: 130.7 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

CRISPR-associated endonuclease Cas9

Geobacillus stearothermophilus

UniProt A0ABF7PG96

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 543–650 Not recorded Anti-CRISPR protein (AcrIIC1) × 1 (A0A2D0TCG3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;0.2 M Sodium malonate pH 6.0, 20% w/v PEG 3,350 Resolution 1.79 Å R-free 0.233
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 543–650 Not recorded Anti-CRISPR protein (AcrIIC1) × 1 (A0A2D0TCG3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;0.2 M Sodium malonate pH 6.0, 20% w/v PEG 3,350 Resolution 1.79 Å R-free 0.233
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain K; UniProt 543–650 Not recorded Anti-CRISPR protein (AcrIIC1) × 1 (A0A2D0TCG3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;0.2 M Sodium malonate pH 6.0, 20% w/v PEG 3,350 Resolution 1.79 Å R-free 0.233
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 543–650 Not recorded Anti-CRISPR protein (AcrIIC1) × 1 (A0A2D0TCG3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;0.2 M Sodium malonate pH 6.0, 20% w/v PEG 3,350 Resolution 1.79 Å R-free 0.233
5 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 543–650 Not recorded Anti-CRISPR protein (AcrIIC1) × 1 (A0A2D0TCG3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;0.2 M Sodium malonate pH 6.0, 20% w/v PEG 3,350 Resolution 1.79 Å R-free 0.233
6 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain I; UniProt 543–650 Not recorded Anti-CRISPR protein (AcrIIC1) × 1 (A0A2D0TCG3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;0.2 M Sodium malonate pH 6.0, 20% w/v PEG 3,350 Resolution 1.79 Å R-free 0.233

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.

1 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0ABF7PG96_GEOSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–111; UniProt 543–650 Author chain C; PDBConstruct 4–111; UniProt 543–650 Author chain E; PDBConstruct 4–111; UniProt 543–650 Author chain G; PDBConstruct 4–111; UniProt 543–650 Author chain I; PDBConstruct 4–111; UniProt 543–650 Author chain K; PDBConstruct 4–111; UniProt 543–650

Anti-CRISPR protein (AcrIIC1)

Neisseria meningitidis

UniProt A0A2D0TCG3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1–86 Not recorded CRISPR-associated endonuclease Cas9 × 1 (A0ABF7PG96) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;0.2 M Sodium malonate pH 6.0, 20% w/v PEG 3,350 Resolution 1.79 Å R-free 0.233
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain L; UniProt 1–86 Not recorded CRISPR-associated endonuclease Cas9 × 1 (A0ABF7PG96) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;0.2 M Sodium malonate pH 6.0, 20% w/v PEG 3,350 Resolution 1.79 Å R-free 0.233
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 1–86 Not recorded CRISPR-associated endonuclease Cas9 × 1 (A0ABF7PG96) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;0.2 M Sodium malonate pH 6.0, 20% w/v PEG 3,350 Resolution 1.79 Å R-free 0.233
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 1–86 Not recorded CRISPR-associated endonuclease Cas9 × 1 (A0ABF7PG96) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;0.2 M Sodium malonate pH 6.0, 20% w/v PEG 3,350 Resolution 1.79 Å R-free 0.233
5 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain H; UniProt 1–86 Not recorded CRISPR-associated endonuclease Cas9 × 1 (A0ABF7PG96) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;0.2 M Sodium malonate pH 6.0, 20% w/v PEG 3,350 Resolution 1.79 Å R-free 0.233
6 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain J; UniProt 1–86 Not recorded CRISPR-associated endonuclease Cas9 × 1 (A0ABF7PG96) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;0.2 M Sodium malonate pH 6.0, 20% w/v PEG 3,350 Resolution 1.79 Å R-free 0.233

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.

4 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A2D0TCG3_NEIME
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–86; UniProt 1–86 Author chain D; PDBConstruct 1–86; UniProt 1–86 Author chain F; PDBConstruct 1–86; UniProt 1–86 Author chain H; PDBConstruct 1–86; UniProt 1–86 Author chain J; PDBConstruct 1–86; UniProt 1–86 Author chain L; PDBConstruct 1–86; UniProt 1–86

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 10vc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 10vc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id10vc
Deposition date deposition_date2026-02-10
最后修订 last_revision2026-04-29
Structure title titleCrystal structure of GeoCas9 HNH domain bound to anti-CRISPR AcrIIC1
Keywords keywordsNuclease, Cas9, Inhibitor, Anti-CRISPR, CRISPR, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier39.55
Radius of gyration Rg (electron density) rg_electron39.32
Forward intensity I(0) i0277250000.00
Molecular weight molecular_weight134140.0 kDa
Excluded volume excluded_volume167350 ų
Envelope volume envelope_volume230700 ų
Hydration-shell volume shell_volume49562 ų
Envelope diameter envelope_diameter141.6
Shell Rg shell_rg44.66
Envelope Rg envelope_rg38.13
Shape Rg shape_rg39.32
Total Rg total_rg39.64
Total atoms total_atoms9450
Residues n_residues1159
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax130.7
Rg (real space) rg_real39.48
Rg uncertainty (real space) rg_real_error1.31
I(0) (real space) i0_real2.7720e+08
I(0) uncertainty (real space) i0_real_error5.1440e+06
Rg (reciprocal space) rg_reciprocal39.53
I(0) (reciprocal space) i0_reciprocal277300000.0000
Solution quality estimate total_estimate0.8719
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary52.3
Skewness Skewness skewness0.243
Kurtosis Kurtosis kurtosis-0.282
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12450000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.870

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)