9jbo

Cryo-EM structure of human SOD1 (WT) amyloid filament

Method: ELECTRON MICROSCOPY Dmax: 93.9 Å Quality: GOOD

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–154 Chain B; UniProt 1–154 Chain C; UniProt 1–154 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.39 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.

153 other PDB entries and 375 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 8–161; UniProt 1–154 Author chain B; PDBConstruct 8–161; UniProt 1–154 Author chain C; PDBConstruct 8–161; UniProt 1–154

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 9jbo

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9jbo
Deposition date deposition_date2024-08-27
Structure title titleCryo-EM structure of human SOD1 (WT) amyloid filament
Keywords keywordsamyloid, filament, superoxide dismutase 1, amyotrophic lateral sclerosis, PROTEIN FIBRIL; PROTEIN FIBRIL
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier25.21
Radius of gyration Rg (electron density) rg_electron24.85
Forward intensity I(0) i012813400.00
Molecular weight molecular_weight26631.0 kDa
Excluded volume excluded_volume33265 ų
Envelope volume envelope_volume43679 ų
Hydration-shell volume shell_volume16582 ų
Envelope diameter envelope_diameter94.5
Shell Rg shell_rg28.59
Envelope Rg envelope_rg25.24
Shape Rg shape_rg24.89
Total Rg total_rg25.25
Total atoms total_atoms1872
Residues n_residues258
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 dmax93.9
Rg (real space) rg_real25.49
Rg uncertainty (real space) rg_real_error0.93
I(0) (real space) i0_real1.2810e+07
I(0) uncertainty (real space) i0_real_error1.9890e+05
Rg (reciprocal space) rg_reciprocal25.40
I(0) (reciprocal space) i0_reciprocal12810000.0000
Solution quality estimate total_estimate0.7971
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.8
Skewness Skewness skewness0.595
Kurtosis Kurtosis kurtosis-0.031
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha926900.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.679; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.410; Smooth: 0.912

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

8. Citations (1)

9. Files and Curves (10)