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9hm7

Cryo-EM structure of apo human separase with the mutation C2029S

Method: ELECTRON MICROSCOPY Dmax: 136.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Separin

Homo sapiens

UniProt Q14674

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–2120 Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 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 9HM7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7NJ0 CryoEM structure of the human Separase-Cdk1-cyclin B1-Cks1 complex Deposited 2021-02-14 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–2120（2120 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7NJ1 CryoEM structure of the human Separase-Securin complex Deposited 2021-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–2120（2120 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9HMA Cryo-EM structure of apo human separase Deposited 2024-12-07 Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–2120（2120 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9HMS Cryo-EM structure of human separase bound to SCC1 (310-550 aa) and SA2 Deposited 2024-12-09 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–1481（1481 aa）
Chain C 1537–2120（584 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9HN0 Cryo-EM structure of human separase bound to SCC1 (310-550 aa) Deposited 2024-12-10 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–1481（1481 aa）
Chain B 1537–2120（584 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9HN4 Cryo-EM structure of human separase bound to phosphorylated SCC1 (310-550 aa) Deposited 2024-12-10 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–1481（1481 aa）
Chain B 1537–2120（584 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
9HN5 Cryo-EM structure of human separase bound to phosphorylated SCC1 (100-320 aa) Deposited 2024-12-10 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1481（1481 aa）
Chain A 1537–2120（584 aa）
Mutation：C2029S Mutation：C2029S ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9HVY Cryo-EM structure of human separase-SCC1 (1-631) fusion protein Deposited 2025-01-02 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–2120（2120 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ESPL1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 58–2177； UniProt 1–2120

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 9hm7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9hm7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9hm7
Deposition date deposition_date2024-12-06
Structure title titleCryo-EM structure of apo human separase with the mutation C2029S
Keywords keywordsSeparase, cell cycle; CELL CYCLE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier39.30 Å
Radius of gyration Rg (electron density) rg_electron38.60 Å
Forward intensity I(0) i0311879000.00
Molecular weight molecular_weight144250.0 kDa
Excluded volume excluded_volume181210 ų
Envelope volume envelope_volume250100 ų
Hydration-shell volume shell_volume55563 ų
Envelope diameter envelope_diameter145.2 Å
Shell Rg shell_rg42.91 Å
Envelope Rg envelope_rg38.92 Å
Shape Rg shape_rg38.66 Å
Total Rg total_rg38.66 Å
Total atoms total_atoms10150
Residues n_residues1340
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 dmax136.6 Å
Rg (real space) rg_real39.62 Å
Rg uncertainty (real space) rg_real_error1.40 Å
I(0) (real space) i0_real3.1190e+08
I(0) uncertainty (real space) i0_real_error6.2960e+06
Rg (reciprocal space) rg_reciprocal39.42 Å
I(0) (reciprocal space) i0_reciprocal311800000.0000
Solution quality estimate total_estimate0.8366
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.0 Å
Skewness Skewness skewness0.575
Kurtosis Kurtosis kurtosis-0.062
Angular range angular_range— – 0.2000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha65220000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.732; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.934; Smooth: 0.743
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)