3gqf

Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q

Method: X-RAY DIFFRACTION Dmax: 150.8 Å Quality: REASONABLE

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

Superoxide dismutase [Cu-Zn]

Homo sapiens

UniProt P00441

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2–154 Chain B; UniProt 2–154 Mutation:H46R, H48Q ZN ZINC ION × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;297 K;20% polyethylene glycol 1000, imidazole pH 8.0, calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 297K Resolution 2.20 Å R-free 0.242
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 2–154 Chain D; UniProt 2–154 Mutation:H46R, H48Q ZN ZINC ION × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;297 K;20% polyethylene glycol 1000, imidazole pH 8.0, calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 297K Resolution 2.20 Å R-free 0.242
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 2–154 Chain F; UniProt 2–154 Mutation:H46R, H48Q ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;297 K;20% polyethylene glycol 1000, imidazole pH 8.0, calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 297K Resolution 2.20 Å R-free 0.242

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.

153 other PDB entries and 373 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SODC_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–153; UniProt 2–154 Author chain B; PDBConstruct 1–153; UniProt 2–154 Author chain C; PDBConstruct 1–153; UniProt 2–154 Author chain D; PDBConstruct 1–153; UniProt 2–154 Author chain E; PDBConstruct 1–153; UniProt 2–154 Author chain F; PDBConstruct 1–153; UniProt 2–154

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 3gqf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3gqf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3gqf
Deposition date deposition_date2009-03-24
Structure title titleStructural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q
Keywords keywords;HUMAN CU-ZN SUPEROXIDE DISMUTASE, SUPEROXIDE ACCEPTOR, FAMILIAL AMYOTROPHIC LATERAL SCLEROSIS MUTANT, Acetylation, Amyotrophic lateral sclerosis, Antioxidant, Copper, Cytoplasm, Disease mutation, Disulfide bond, Metal-binding, Oxidoreductase, Phosphoprotein, Ubl conjugation, Zinc ;; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier45.88
Radius of gyration Rg (electron density) rg_electron46.29
Forward intensity I(0) i0155395000.00
Molecular weight molecular_weight95450.0 kDa
Excluded volume excluded_volume116800 ų
Envelope volume envelope_volume180530 ų
Hydration-shell volume shell_volume34563 ų
Envelope diameter envelope_diameter156.3
Shell Rg shell_rg47.07
Envelope Rg envelope_rg44.72
Shape Rg shape_rg46.29
Total Rg total_rg46.32
Total atoms total_atoms6671
Residues n_residues918
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 dmax150.8
Rg (real space) rg_real46.41
Rg uncertainty (real space) rg_real_error1.54
I(0) (real space) i0_real1.5540e+08
I(0) uncertainty (real space) i0_real_error2.9970e+06
Rg (reciprocal space) rg_reciprocal45.89
I(0) (reciprocal space) i0_reciprocal155300000.0000
Solution quality estimate total_estimate0.5032
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.6
Skewness Skewness skewness0.330
Kurtosis Kurtosis kurtosis-0.941
Angular range angular_range— – 0.1700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5738000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.472; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.378; Smooth: 0.397

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd3gqfa_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.8 — Cu,Zn superoxide dismutase-like
Family Family familyb.1.8.1 — Cu,Zn superoxide dismutase-like
Domain ID domain_idd3gqfb_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.8 — Cu,Zn superoxide dismutase-like
Family Family familyb.1.8.1 — Cu,Zn superoxide dismutase-like
Domain ID domain_idd3gqfc_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.8 — Cu,Zn superoxide dismutase-like
Family Family familyb.1.8.1 — Cu,Zn superoxide dismutase-like
Domain ID domain_idd3gqfd_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.8 — Cu,Zn superoxide dismutase-like
Family Family familyb.1.8.1 — Cu,Zn superoxide dismutase-like
Domain ID domain_idd3gqfe_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.8 — Cu,Zn superoxide dismutase-like
Family Family familyb.1.8.1 — Cu,Zn superoxide dismutase-like
Domain ID domain_idd3gqff_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.8 — Cu,Zn superoxide dismutase-like
Family Family familyb.1.8.1 — Cu,Zn superoxide dismutase-like

CATH v4.4 (6 domains)

Domain ID domain_id3gqfA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily200 — Superoxide dismutase, copper/zinc binding domain
Domain ID domain_id3gqfB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily200 — Superoxide dismutase, copper/zinc binding domain
Domain ID domain_id3gqfC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily200 — Superoxide dismutase, copper/zinc binding domain
Domain ID domain_id3gqfD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily200 — Superoxide dismutase, copper/zinc binding domain
Domain ID domain_id3gqfE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily200 — Superoxide dismutase, copper/zinc binding domain
Domain ID domain_id3gqfF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily200 — Superoxide dismutase, copper/zinc binding domain

8. Citations (1)

9. Files and Curves (10)