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4j1y

The X-ray crystal structure of human complement protease C1s zymogen

Method: X-RAY DIFFRACTION Dmax: 154.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Complement C1s subcomponent

Homo sapiens

UniProt P09871

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 292–688 Fragment：CCP1-CCP2-SPz (UNP Residues 292-698) Mutation：Q436A, I438A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；18% PEG 3350, 0.2M potassium nitrate., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.66 Å R-free 0.259
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 292–688 Fragment：CCP1-CCP2-SPz (UNP Residues 292-698) Mutation：Q436A, I438A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；18% PEG 3350, 0.2M potassium nitrate., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.66 Å R-free 0.259
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 292–688 Chain B； UniProt 292–688 Fragment：CCP1-CCP2-SPz (UNP Residues 292-698) Mutation：Q436A, I438A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；18% PEG 3350, 0.2M potassium nitrate., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.66 Å R-free 0.259

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 4J1Y Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1ELV CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN COMPLEMENT C1S PROTEASE Deposited 2000-03-14 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: monomeric
Chain A 358–688（331 aa） Fragment：CCP2-SP CATALYTIC FRAGMENT: ASP363-ASP-673 SEGMENT PRECEDED BY AN ASP-LEU SEQUENCE ADDED AT THE N-TERMINAL END
Mutation：YES SO4 SULFATE ION × 2 NES 2-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；PEG 4K 34%, AMMONIUM SULFATE 100mM, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.70 Å R-free 0.219
1NZI Crystal Structure of the CUB1-EGF Interaction Domain of Complement Protease C1s Deposited 2003-02-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 16–174（159 aa） Fragment：CALCIUM-DEPENDENT INTERACTION DOMAIN
Chain B 16–174（159 aa） Fragment：CALCIUM-DEPENDENT INTERACTION DOMAIN
Not recorded CA CALCIUM ION × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 4000, magnesium chloride, glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.50 Å R-free 0.234
4LMF C1s CUB1-EGF-CUB2 Deposited 2013-07-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 17–292（276 aa） Fragment：CUB1-EGF-CUB2 fragment (unp residues 17-292)
Not recorded NA SODIUM ION × 1 CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.92 Å R-free 0.252
4LMF C1s CUB1-EGF-CUB2 Deposited 2013-07-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 17–292（276 aa） Fragment：CUB1-EGF-CUB2 fragment (unp residues 17-292)
Not recorded NA SODIUM ION × 1 CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.92 Å R-free 0.252
4LMF C1s CUB1-EGF-CUB2 Deposited 2013-07-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 17–292（276 aa） Fragment：CUB1-EGF-CUB2 fragment (unp residues 17-292)
Not recorded NA SODIUM ION × 1 CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.92 Å R-free 0.252
4LMF C1s CUB1-EGF-CUB2 Deposited 2013-07-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 17–292（276 aa） Fragment：CUB1-EGF-CUB2 fragment (unp residues 17-292)
Not recorded NA SODIUM ION × 1 CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.92 Å R-free 0.252
4LMF C1s CUB1-EGF-CUB2 Deposited 2013-07-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 17–292（276 aa） Fragment：CUB1-EGF-CUB2 fragment (unp residues 17-292)
Chain D 17–292（276 aa） Fragment：CUB1-EGF-CUB2 fragment (unp residues 17-292)
Not recorded NA SODIUM ION × 2 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.92 Å R-free 0.252
4LMF C1s CUB1-EGF-CUB2 Deposited 2013-07-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 17–292（276 aa） Fragment：CUB1-EGF-CUB2 fragment (unp residues 17-292)
Chain C 17–292（276 aa） Fragment：CUB1-EGF-CUB2 fragment (unp residues 17-292)
Not recorded NA SODIUM ION × 2 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.92 Å R-free 0.252
4LOR C1s CUB1-EGF-CUB2 in complex with a collagen-like peptide from C1q Deposited 2013-07-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 17–292（276 aa） Fragment：CUB1-EGF-CUB2 fragment (unp residues 17-292)
Not recorded CA CALCIUM ION × 3 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100 mM Tris, 100 mM NaBr, 24% PEG 3350 , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.50 Å R-free 0.252
4LOS C1s CUB2-CCP1 Deposited 2013-07-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 172–358（187 aa） Fragment：CUB2-CCP1 fragment (unp residues 172-358)
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；100 mM Tris/acetate, 200 mM KH2PO4 + 20% PEG 10K , pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.212
4LOT C1s CUB2-CCP1-CCP2 Deposited 2013-07-13 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 175–423（249 aa） Fragment：CUB2-CCP1-CCP2 fragment (unp residues 175-423)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；293 K；24% PEG 8K in Bis-tris propane-HCL, containing 200 mM potassium citrate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.92 Å R-free 0.292
5UBM Crystal structure of human C1s in complex with inhibitor gigastasin Deposited 2016-12-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 437–688（252 aa）
Chain B 285–436（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；0.1 M Bis-Tris, pH 5.5, 25 % PEG 3350
Resolution 2.50 Å R-free 0.222
6F1C C1rC1s complex Deposited 2017-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 16–292（277 aa）
Chain D 16–292（277 aa）
Not recorded CA CALCIUM ION × 12 NA SODIUM ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；12-18% PEG 8000, 100 mM Imidazole at pH 8.0
Resolution 4.20 Å R-free 0.305
6F1H C1rC1s complex Deposited 2017-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 17–292（276 aa）
Not recorded CA CALCIUM ION × 6 NA SODIUM ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；12-18% PEG 8000, 100 mM Imidazole at pH 8.0
Resolution 4.50 Å R-free 0.340
6F1H C1rC1s complex Deposited 2017-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 17–292（276 aa）
Not recorded CA CALCIUM ION × 6 NA SODIUM ION × 3 LYS LYSINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；12-18% PEG 8000, 100 mM Imidazole at pH 8.0
Resolution 4.50 Å R-free 0.340
8GMN Crystal structure of human C1s in complex with inhibitor Deposited 2023-03-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 358–688（331 aa）
Not recorded ZWK [4-(1-aminophthalazin-6-yl)piperazin-1-yl](2-methylphenyl)methanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；22% PEG 3350, 50-100 mM Ammonium Sulphate and 100 mM TRIS pH 7.5-8.0
Resolution 2.60 Å R-free 0.281
8GMN Crystal structure of human C1s in complex with inhibitor Deposited 2023-03-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 358–688（331 aa）
Not recorded ZWK [4-(1-aminophthalazin-6-yl)piperazin-1-yl](2-methylphenyl)methanone × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；22% PEG 3350, 50-100 mM Ammonium Sulphate and 100 mM TRIS pH 7.5-8.0
Resolution 2.60 Å R-free 0.281
8GMN Crystal structure of human C1s in complex with inhibitor Deposited 2023-03-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 358–688（331 aa）
Not recorded ZWK [4-(1-aminophthalazin-6-yl)piperazin-1-yl](2-methylphenyl)methanone × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；22% PEG 3350, 50-100 mM Ammonium Sulphate and 100 mM TRIS pH 7.5-8.0
Resolution 2.60 Å R-free 0.281
8GMN Crystal structure of human C1s in complex with inhibitor Deposited 2023-03-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 358–688（331 aa）
Not recorded ZWK [4-(1-aminophthalazin-6-yl)piperazin-1-yl](2-methylphenyl)methanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；22% PEG 3350, 50-100 mM Ammonium Sulphate and 100 mM TRIS pH 7.5-8.0
Resolution 2.60 Å R-free 0.281
8TYP Complement Protease C1s Inhibited by 6-(4-phenylpiperazin-1-yl)pyridine-3-carboximidamide Deposited 2023-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 358–688（331 aa）
Not recorded SQT 6-(4-phenylpiperazin-1-yl)pyridine-3-carboximidamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium acetate 0.1 M Tris-HCl (pH 8.1) PEG-4000 24% (w/v)
Resolution 1.80 Å R-free 0.196
8W18 The crystal structure of the Michaelis-Menten complex of a C1s/C1-INH at 3.94 Angstroms Deposited 2024-02-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 292–437（146 aa） Fragment：Sushi domains
Chain B 438–688（251 aa）
Mutation：S632A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M L-Proline, 0.1M HEPES (pH 6.5), and 12% PEG 3,350
Resolution 3.94 Å R-free 0.281
9X1H Cryo-EM Structure of human complement C1s CUB domain in complex with RAY121 Deposited 2025-10-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 16–292（277 aa）
Chain B 16–292（277 aa）
Not recorded CA CALCIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM HEPES(7.5), 150mM NaCl, 3mM CaCl2, 0.03% DDM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å

13 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C1S_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–397； UniProt 292–688 Author chain B； PDBConstruct 1–397； UniProt 292–688

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 4j1y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4j1y
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4j1y
Deposition date deposition_date2013-02-03
Structure title titleThe X-ray crystal structure of human complement protease C1s zymogen
Keywords keywordsC4, C2, Hydrolysis, Extracellular, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.88 Å
Radius of gyration Rg (electron density) rg_electron37.34 Å
Forward intensity I(0) i0103415000.00
Molecular weight molecular_weight79442.0 kDa
Excluded volume excluded_volume98558 ų
Envelope volume envelope_volume139530 ų
Hydration-shell volume shell_volume34767 ų
Envelope diameter envelope_diameter163.9 Å
Shell Rg shell_rg38.31 Å
Envelope Rg envelope_rg38.14 Å
Shape Rg shape_rg37.28 Å
Total Rg total_rg37.60 Å
Total atoms total_atoms5581
Residues n_residues741
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 dmax154.2 Å
Rg (real space) rg_real37.38 Å
Rg uncertainty (real space) rg_real_error2.29 Å
I(0) (real space) i0_real1.0340e+08
I(0) uncertainty (real space) i0_real_error2.0310e+06
Rg (reciprocal space) rg_reciprocal37.06 Å
I(0) (reciprocal space) i0_reciprocal103400000.0000
Solution quality estimate total_estimate0.7235
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.6 Å
Skewness Skewness skewness0.706
Kurtosis Kurtosis kurtosis0.729
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11480000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.415; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.302; Smooth: 0.855
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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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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4j1yA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id4j1yA03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id4j1yB02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id4j1yB03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
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8. Citations (1)

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9. Files and Curves (10)