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8cx3

Crystal structure of full-length mesothelin

Method: X-RAY DIFFRACTION Dmax: 174.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 4 of Mesothelin

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 295–599 Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.2；289 K；0.9-1.1 M sodium/potassium phosphate, pH 8.2 Resolution 3.61 Å R-free 0.310
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 295–599 Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.2；289 K；0.9-1.1 M sodium/potassium phosphate, pH 8.2 Resolution 3.61 Å R-free 0.310
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 295–599 Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.2；289 K；0.9-1.1 M sodium/potassium phosphate, pH 8.2 Resolution 3.61 Å R-free 0.310
4 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 295–599 Not recorded 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.2；289 K；0.9-1.1 M sodium/potassium phosphate, pH 8.2 Resolution 3.61 Å R-free 0.310
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain E； UniProt 295–599 Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.2；289 K；0.9-1.1 M sodium/potassium phosphate, pH 8.2 Resolution 3.61 Å R-free 0.310
6 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain F； UniProt 295–599 Not recorded beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.2；289 K；0.9-1.1 M sodium/potassium phosphate, pH 8.2 Resolution 3.61 Å R-free 0.310

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.

Other PDB Difference from Current Entry 8CX3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4F3F Crystal Structure of Msln7-64 MORAb-009 FAB complex Deposited 2012-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 302–359（58 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；0.1 M Trisodium citrate pH 5.6, 17% Polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.65 Å R-free 0.222
7U8C Crystal structure of Mesothelin C-terminal peptide-MORAb 15B6 FAB complex Deposited 2022-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain BA2 590–606（17 aa） Fragment：C-terminal peptide (UNP residues 590-606)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M sodium acetate, pH 4.5, 26% PEG550 MME, 6% 2-propanol
Resolution 1.74 Å R-free 0.238
7U9J Crystal structure of Mesothelin-207 fragment Deposited 2022-03-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 296–501（206 aa）
Not recorded SO4 SULFATE ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M HEPES, pH 7.5, 100 mM potassium chloride, 12.5% PEG3350, 100 mM lithium sulfate
Resolution 2.09 Å R-free 0.216
7U9J Crystal structure of Mesothelin-207 fragment Deposited 2022-03-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 296–501（206 aa）
Not recorded SO4 SULFATE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M HEPES, pH 7.5, 100 mM potassium chloride, 12.5% PEG3350, 100 mM lithium sulfate
Resolution 2.09 Å R-free 0.216
7UED Crystal structure of full length mesothelin bound with MORAb-009 Fab Deposited 2022-03-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain M 295–599（305 aa）
Not recorded GOL GLYCEROL × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；0.1 M Tris, pH 7, 150 mM sodium citrate, 16.4% PEG3350, 100 mM lithium sulfate
Resolution 3.00 Å R-free 0.237
8CXC Novel Anti-Mesothelin Antibodies Enable Crystallography of the Intact Mesothelin Ectodo- main and Engineering of Potent, T cell-engaging Bispecific Therapeutics Deposited 2022-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: pentameric
Chain M 296–605（310 aa）
Not recorded No recorded non-water small molecule 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
8CYH Novel Anti-Mesothelin Antibodies Enable Crystallography of the Intact Mesothelin Ectodo- main and Engineering of Potent, T cell-engaging Bispecific Therapeutics Deposited 2022-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain M 296–605（310 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Tris (8.0), sodium citrate, Peg3350
Resolution 3.38 Å R-free 0.268
8CZ8 Novel Anti-Mesothelin Antibodies Enable Crystallography of the Intact Mesothelin Ectodo- main and Engineering of Potent, T cell-engaging Bispecific Therapeutics Deposited 2022-05-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 434–590（157 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；bicine (9.0), glycerol, ammonium sulfate
Resolution 2.60 Å R-free 0.224
8CZ8 Novel Anti-Mesothelin Antibodies Enable Crystallography of the Intact Mesothelin Ectodo- main and Engineering of Potent, T cell-engaging Bispecific Therapeutics Deposited 2022-05-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain M 434–590（157 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；bicine (9.0), glycerol, ammonium sulfate
Resolution 2.60 Å R-free 0.224
8FSL Human Mesothelin bound to a neutralizing VH domain antibody Deposited 2023-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 300–584（285 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；286 K；PEG3350 20% 0.15 M ammonium nitrate
Resolution 2.90 Å R-free 0.254
8FSL Human Mesothelin bound to a neutralizing VH domain antibody Deposited 2023-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 300–584（285 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；286 K；PEG3350 20% 0.15 M ammonium nitrate
Resolution 2.90 Å R-free 0.254
8VM1 Structural Elucidation of the Mesothelin Mucin16 CA125 Interaction Deposited 2024-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 296–359（64 aa） Fragment：residues 296-359 of mesothelin (Uniprot numbering),SEA 10 domain of mucin-16
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Bis-Tris, NH4CL, PEG3350
Resolution 2.65 Å R-free 0.298
9P4C Crystal structure of Mesothelin C-terminal peptide-RO4 Fab complex Deposited 2025-06-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain M 590–606（17 aa） Fragment：C-terminal peptide (UNP residues 590-606)
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Bis-Tris, pH 6.5 and 16% PEG 10000
Resolution 1.52 Å R-free 0.180
9Z3B Structure C-terminal human Mesothelin Peptide bound to MSLNB703 Fab Deposited 2025-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 590–606（17 aa） Fragment：C-terminal peptide (UNP residues 590-606)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG1500
Resolution 1.96 Å R-free 0.278
9Z3B Structure C-terminal human Mesothelin Peptide bound to MSLNB703 Fab Deposited 2025-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 590–606（17 aa） Fragment：C-terminal peptide (UNP residues 590-606)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG1500
Resolution 1.96 Å R-free 0.278
9Z3B Structure C-terminal human Mesothelin Peptide bound to MSLNB703 Fab Deposited 2025-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 590–606（17 aa） Fragment：C-terminal peptide (UNP residues 590-606)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG1500
Resolution 1.96 Å R-free 0.278
9Z3B Structure C-terminal human Mesothelin Peptide bound to MSLNB703 Fab Deposited 2025-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 590–606（17 aa） Fragment：C-terminal peptide (UNP residues 590-606)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG1500
Resolution 1.96 Å R-free 0.278

11 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MSLN_HUMAN
Isoform Q13421-4
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–306； UniProt 295–599 Author chain B； PDBConstruct 2–306； UniProt 295–599 Author chain C； PDBConstruct 2–306； UniProt 295–599 Author chain D； PDBConstruct 2–306； UniProt 295–599 Author chain E； PDBConstruct 2–306； UniProt 295–599 Author chain F； PDBConstruct 2–306； UniProt 295–599

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 8cx3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8cx3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8cx3
Deposition date deposition_date2022-05-19
Structure title titleCrystal structure of full-length mesothelin
Keywords keywordsMesothelin, CELL ADHESION; CELL ADHESION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier65.98 Å
Radius of gyration Rg (electron density) rg_electron65.68 Å
Forward intensity I(0) i0392609000.00
Molecular weight molecular_weight170330.0 kDa
Excluded volume excluded_volume214690 ų
Envelope volume envelope_volume434750 ų
Hydration-shell volume shell_volume56762 ų
Envelope diameter envelope_diameter181.6 Å
Shell Rg shell_rg70.28 Å
Envelope Rg envelope_rg58.76 Å
Shape Rg shape_rg65.68 Å
Total Rg total_rg65.77 Å
Total atoms total_atoms11960
Residues n_residues1485
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax174.8 Å
Rg (real space) rg_real65.66 Å
Rg uncertainty (real space) rg_real_error1.37 Å
I(0) (real space) i0_real3.9260e+08
I(0) uncertainty (real space) i0_real_error7.9950e+06
Rg (reciprocal space) rg_reciprocal66.15 Å
I(0) (reciprocal space) i0_reciprocal392900000.0000
Solution quality estimate total_estimate0.7839
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary116.5 Å
Skewness Skewness skewness-0.202
Kurtosis Kurtosis kurtosis-1.068
Angular range angular_range— – 0.1200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11640000.0000
Real-space data points n_real_points25
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.748; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)