SAXSdb — 7u9j

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

Isoform 3 of Mesothelin

Homo sapiens

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 296–501	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 296–501	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

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 7U9J	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
7UED Crystal structure of full length mesothelin bound with MORAb-009 Fab Deposited 2022-03-21	Different construct Different oligomeric state 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
8CX3 Crystal structure of full-length mesothelin Deposited 2022-05-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 295–599（305 aa）	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
8CX3 Crystal structure of full-length mesothelin Deposited 2022-05-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 295–599（305 aa）	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
8CX3 Crystal structure of full-length mesothelin Deposited 2022-05-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 295–599（305 aa）	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
8CX3 Crystal structure of full-length mesothelin Deposited 2022-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain D 295–599（305 aa）	Not recorded	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
8CX3 Crystal structure of full-length mesothelin Deposited 2022-05-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 295–599（305 aa）	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
8CX3 Crystal structure of full-length mesothelin Deposited 2022-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain F 295–599（305 aa）	Not recorded	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
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 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MSLN_HUMAN
Isoform	Q13421-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–207； UniProt 296–501 Author chain B； PDBConstruct 2–207； UniProt 296–501

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7u9j
Deposition date deposition_date	2022-03-10
Structure title title	Crystal structure of Mesothelin-207 fragment
Keywords keywords	Mesothelin, CELL ADHESION; CELL ADHESION
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	27.91 Å
Radius of gyration Rg (electron density) rg_electron	27.10 Å
Forward intensity I(0) i0	38385000.00
Molecular weight molecular_weight	48451.0 kDa
Excluded volume excluded_volume	60755 Å³
Envelope volume envelope_volume	77696 Å³
Hydration-shell volume shell_volume	24984 Å³
Envelope diameter envelope_diameter	104.0 Å
Shell Rg shell_rg	32.84 Å
Envelope Rg envelope_rg	27.17 Å
Shape Rg shape_rg	27.04 Å
Total Rg total_rg	27.91 Å
Total atoms total_atoms	6755
Residues n_residues	418
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	100.9 Å
Rg (real space) rg_real	28.03 Å
Rg uncertainty (real space) rg_real_error	1.23 Å
I(0) (real space) i0_real	3.8390e+07
I(0) uncertainty (real space) i0_real_error	6.4540e+05
Rg (reciprocal space) rg_reciprocal	28.00 Å
I(0) (reciprocal space) i0_reciprocal	38380000.0000
Solution quality estimate total_estimate	0.8508
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.4 Å
Skewness Skewness skewness	0.429
Kurtosis Kurtosis kurtosis	-0.189
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11250000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.747; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.823; Smooth: 0.994

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Isoform 3 of Mesothelin
Molecular weight formula_weight	24437.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7213

MEVEKTACPSGKKAREIDESLIFYKKWELEACVDAALLATQMDRVNAIPFTYEQLDVLKHKLDELYPQGYPESVIQHLGYLFLKMSPEDIRKWNVTSLETLKALLEVNKGHEMSPQVATLIDRFVKGRGQLDKDTLDTLTAFYPGYLCSLSPEELSSVPPSSIWAVRPQDLDTCDPRQLDVLYPKARLAFQNMNGSEYFVKIQSFLGHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	458

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8. Citations (1)

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Unit-cell length a length_a	96.762 Å
Unit-cell length b length_b	78.611 Å
Unit-cell length c length_c	74.332 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.15 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	2.090 Å
Low-resolution limit resolution_low	33.990 Å
R factor r_factor	0.1728
R_work r_work	0.1705
R_free r_free	0.2163

fit	/app/data/saxs_computation/u9/7u9j/7u9j.fit
pddf	/app/data/pr_computation/u9/7u9j/7u9j.pr.out
profile	/app/data/saxs_computation/u9/7u9j/7u9j.dat

Crystal structure of Mesothelin-207 fragment

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

Isoform 3 of Mesothelin

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction