8cxc

Novel Anti-Mesothelin Antibodies Enable Crystallography of the Intact Mesothelin Ectodo- main and Engineering of Potent, T cell-engaging Bispecific Therapeutics

Method: X-RAY DIFFRACTION Dmax: 123.3 Å Quality: GOOD

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

Mesothelin, cleaved form

Homo sapiens

UniProt Q13421

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 heterocomplex Heteromer Protein × 4 PDB declaration: pentameric(5) Count mismatch; review required Chain M; UniProt 296–605 Not recorded 3F2 Antibody light chain × 1 3F2 Antibody heavy chain × 1 scFv Amatuximab × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;293 K;tris 8.0, zinc chloride, ammonium sulfate Resolution 4.31 Å R-free 0.300

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 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MSLN_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain M; PDBConstruct 1–310; UniProt 296–605

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 8cxc

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8cxc
Deposition date deposition_date2022-05-20
Structure title titleNovel Anti-Mesothelin Antibodies Enable Crystallography of the Intact Mesothelin Ectodo- main and Engineering of Potent, T cell-engaging Bispecific Therapeutics
Keywords keywordsAntibody, complex, tumor associated antigen, ANTITUMOR PROTEIN; ANTITUMOR PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier43.71
Radius of gyration Rg (electron density) rg_electron43.27
Forward intensity I(0) i0150141000.00
Molecular weight molecular_weight99140.0 kDa
Excluded volume excluded_volume123530 ų
Envelope volume envelope_volume192530 ų
Hydration-shell volume shell_volume37612 ų
Envelope diameter envelope_diameter131.0
Shell Rg shell_rg48.02
Envelope Rg envelope_rg41.34
Shape Rg shape_rg43.25
Total Rg total_rg43.59
Total atoms total_atoms6984
Residues n_residues938
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 dmax123.3
Rg (real space) rg_real43.80
Rg uncertainty (real space) rg_real_error0.87
I(0) (real space) i0_real1.5010e+08
I(0) uncertainty (real space) i0_real_error2.7580e+06
Rg (reciprocal space) rg_reciprocal43.71
I(0) (reciprocal space) i0_reciprocal150100000.0000
Solution quality estimate total_estimate0.8243
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.8
Skewness Skewness skewness0.151
Kurtosis Kurtosis kurtosis-0.967
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8352000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.802; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)