8r4a

Cryo-EM structure of the D87G lysozyme amyloid fibril

Method: ELECTRON MICROSCOPY Dmax: 108.0 Å Quality: GOOD

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

Lysozyme C

OrganismNot specified

UniProt P61626

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 × 9 PDB declaration: nonameric(9) Consistent with protein copy count Chain A; UniProt 19–148 Chain B; UniProt 19–148 Chain C; UniProt 19–148 Chain D; UniProt 19–148 Chain E; UniProt 19–148 Chain F; UniProt 19–148 Chain G; UniProt 19–148 Chain H; UniProt 19–148 Chain I; UniProt 19–148 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer:pH 7;pure water cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 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.

201 other PDB entries and 219 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYSC_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–130; UniProt 19–148 Author chain B; PDBConstruct 1–130; UniProt 19–148 Author chain C; PDBConstruct 1–130; UniProt 19–148 Author chain D; PDBConstruct 1–130; UniProt 19–148 Author chain E; PDBConstruct 1–130; UniProt 19–148 Author chain F; PDBConstruct 1–130; UniProt 19–148 Author chain G; PDBConstruct 1–130; UniProt 19–148 Author chain H; PDBConstruct 1–130; UniProt 19–148 Author chain I; PDBConstruct 1–130; UniProt 19–148

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 8r4a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8r4a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8r4a
Deposition date deposition_date2023-11-13
Structure title titleCryo-EM structure of the D87G lysozyme amyloid fibril
Keywords keywordsLysozyme, amyloid fibril, misfolding disease, cryo-EM, ALys amyloidosis, amyloidogenic variant, PROTEIN FIBRIL; PROTEIN FIBRIL
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier32.14
Radius of gyration Rg (electron density) rg_electron31.81
Forward intensity I(0) i0307195000.00
Molecular weight molecular_weight131870.0 kDa
Excluded volume excluded_volume161160 ų
Envelope volume envelope_volume185760 ų
Hydration-shell volume shell_volume47909 ų
Envelope diameter envelope_diameter113.0
Shell Rg shell_rg39.54
Envelope Rg envelope_rg31.96
Shape Rg shape_rg31.72
Total Rg total_rg32.58
Total atoms total_atoms9225
Residues n_residues1170
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 dmax108.0
Rg (real space) rg_real32.17
Rg uncertainty (real space) rg_real_error0.85
I(0) (real space) i0_real3.0720e+08
I(0) uncertainty (real space) i0_real_error4.9830e+06
Rg (reciprocal space) rg_reciprocal32.16
I(0) (reciprocal space) i0_reciprocal307200000.0000
Solution quality estimate total_estimate0.8698
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.3
Skewness Skewness skewness0.425
Kurtosis Kurtosis kurtosis-0.187
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha36080000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.889

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

8. Citations (1)

9. Files and Curves (10)