2qy0

Active dimeric structure of the catalytic domain of C1r reveals enzyme-product like contacts

Method: X-RAY DIFFRACTION Dmax: 125.5 Å Quality: GOOD

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

Complement C1r subcomponent

Homo sapiens

UniProt P00736

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 309–463 Chain B; UniProt 464–705 Chain C; UniProt 309–463 Chain D; UniProt 464–705 Fragment:Sushi-1 and Sushi-2 domains, CCP1-CCP2 Fragment:Peptidase S1 domain GOL GLYCEROL × 7 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;288 K;14% (w/v) PEG 6000, 0.2 M NaCl, 10% (v/v) glycerol, 0.1 M Tris HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 288K Resolution 2.60 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.

11 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C1R_HUMAN
Isoform
PDB entities 1, 2
Chains and sequence ranges Author chain A; PDBConstruct 5–159; UniProt 309–463 Author chain C; PDBConstruct 5–159; UniProt 309–463 Author chain B; PDBConstruct 1–242; UniProt 464–705 Author chain D; PDBConstruct 1–242; UniProt 464–705

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 2qy0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2qy0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2qy0
Deposition date deposition_date2007-08-13
Structure title titleActive dimeric structure of the catalytic domain of C1r reveals enzyme-product like contacts
Keywords keywords;complement, serine protease, beta barrel, Complement pathway, EGF-like domain, Glycoprotein, Hydrolase, Hydroxylation, Immune response, Innate immunity, Phosphorylation, Sushi ;; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier38.35
Radius of gyration Rg (electron density) rg_electron38.12
Forward intensity I(0) i0119636000.00
Molecular weight molecular_weight87013.0 kDa
Excluded volume excluded_volume108080 ų
Envelope volume envelope_volume150250 ų
Hydration-shell volume shell_volume34315 ų
Envelope diameter envelope_diameter125.3
Shell Rg shell_rg42.63
Envelope Rg envelope_rg36.70
Shape Rg shape_rg38.12
Total Rg total_rg38.42
Total atoms total_atoms6120
Residues n_residues780
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 dmax125.5
Rg (real space) rg_real38.61
Rg uncertainty (real space) rg_real_error1.12
I(0) (real space) i0_real1.1960e+08
I(0) uncertainty (real space) i0_real_error2.0350e+06
Rg (reciprocal space) rg_reciprocal38.45
I(0) (reciprocal space) i0_reciprocal119600000.0000
Solution quality estimate total_estimate0.8524
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.7
Skewness Skewness skewness0.332
Kurtosis Kurtosis kurtosis-0.793
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8498000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.800; Smooth: 0.768

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd2qy0a1
Class classg — Small proteins
Fold Fold foldg.18 — Complement control module/SCR domain
Superfamily Superfamily superfamilyg.18.1 — Complement control module/SCR domain
Family Family familyg.18.1.1 — Complement control module/SCR domain
Domain ID domain_idd2qy0a2
Class classg — Small proteins
Fold Fold foldg.18 — Complement control module/SCR domain
Superfamily Superfamily superfamilyg.18.1 — Complement control module/SCR domain
Family Family familyg.18.1.1 — Complement control module/SCR domain
Domain ID domain_idd2qy0a3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2qy0b_
Class classb — All beta proteins
Fold Fold foldb.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamilyb.47.1 — Trypsin-like serine proteases
Family Family familyb.47.1.0 — automated matches
Domain ID domain_idd2qy0c1
Class classg — Small proteins
Fold Fold foldg.18 — Complement control module/SCR domain
Superfamily Superfamily superfamilyg.18.1 — Complement control module/SCR domain
Family Family familyg.18.1.1 — Complement control module/SCR domain
Domain ID domain_idd2qy0c2
Class classg — Small proteins
Fold Fold foldg.18 — Complement control module/SCR domain
Superfamily Superfamily superfamilyg.18.1 — Complement control module/SCR domain
Family Family familyg.18.1.1 — Complement control module/SCR domain
Domain ID domain_idd2qy0c3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2qy0d_
Class classb — All beta proteins
Fold Fold foldb.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamilyb.47.1 — Trypsin-like serine proteases
Family Family familyb.47.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id2qy0A01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology70 — Complement Module; domain 1
Homologous superfamily homologous superfamily10 — Complement Module, domain 1
Domain ID domain_id2qy0A02
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology70 — Complement Module; domain 1
Homologous superfamily homologous superfamily10 — Complement Module, domain 1
Domain ID domain_id2qy0B01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id2qy0B02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id2qy0C01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology70 — Complement Module; domain 1
Homologous superfamily homologous superfamily10 — Complement Module, domain 1
Domain ID domain_id2qy0C02
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology70 — Complement Module; domain 1
Homologous superfamily homologous superfamily10 — Complement Module, domain 1
Domain ID domain_id2qy0D01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id2qy0D02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases

8. Citations (1)

9. Files and Curves (10)