SAXSdb — 9p4c

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

Mesothelin, cleaved form

OrganismNot specified

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain M； UniProt 590–606	Fragment：C-terminal peptide (UNP residues 590-606)	Light chain of the RO4 Fab fragment × 1 Heavy chain of the RO4 fab fragment × 1 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

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 9P4C	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 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 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 oligomeric state 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 oligomeric state 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 construct 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
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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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
9Z3B Structure C-terminal human Mesothelin Peptide bound to MSLNB703 Fab Deposited 2025-11-06	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 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 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 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 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 1–17； UniProt 590–606

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	9p4c
Deposition date deposition_date	2025-06-16
Structure title title	Crystal structure of Mesothelin C-terminal peptide-RO4 Fab complex
Keywords keywords	Mesothelin, antibody, IMMUNE SYSTEM, ANTITUMOR PROTEIN; ANTITUMOR PROTEIN
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	24.97 Å
Radius of gyration Rg (electron density) rg_electron	24.14 Å
Forward intensity I(0) i0	36488300.00
Molecular weight molecular_weight	46273.0 kDa
Excluded volume excluded_volume	57674 Å³
Envelope volume envelope_volume	70671 Å³
Hydration-shell volume shell_volume	24597 Å³
Envelope diameter envelope_diameter	86.3 Å
Shell Rg shell_rg	30.97 Å
Envelope Rg envelope_rg	24.03 Å
Shape Rg shape_rg	24.10 Å
Total Rg total_rg	25.01 Å
Total atoms total_atoms	6430
Residues n_residues	443
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	86.8 Å
Rg (real space) rg_real	24.96 Å
Rg uncertainty (real space) rg_real_error	0.91 Å
I(0) (real space) i0_real	3.6490e+07
I(0) uncertainty (real space) i0_real_error	5.3080e+05
Rg (reciprocal space) rg_reciprocal	24.96 Å
I(0) (reciprocal space) i0_reciprocal	36490000.0000
Solution quality estimate total_estimate	0.7838
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.8 Å
Skewness Skewness skewness	0.303
Kurtosis Kurtosis kurtosis	-0.430
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8407000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.770; Stabil: 0.987; Sysdev: 1.000; Positv: 1.000; Valcen: 0.914; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Light chain of the RO4 Fab fragment
Molecular weight formula_weight	22506.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	7172

ADVVMTQTPSSVSAAVGGTVTMKCQASQSISTALVWYQQKPGQPPKLLIRSTSTLASGVPSRFKGSGSGTQFTLTISDLECADAATYYCQSAALIGGVVFGAFGGGTEVVVRGDPVAPTVLIFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSSTLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC

来源 Source

来源生物 organism	Oryctolagus cuniculus
NCBI Class编号 ncbi_taxonomy_id	9986
宿主生物 host_organism	Oryctolagus cuniculus

Entity 2 Entity 2 polymer

Description description	Heavy chain of the RO4 fab fragment
Molecular weight formula_weight	21892.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QSLEESGGGLVTPGGILTLTCTASGFDISRHYMTWVRQAPGEGLEWIGSIYGGSTYYASWAKGRFTISKTSSTTVDLKMTSLTTEDTATYFCVRGVGGGLWGPGTLVTVSSGQPKAPSVFPLAPCCGDTPSSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSVVSVTSSSQPVTCNVAHPATNTKVDKTVAPSTC

来源 Source

来源生物 organism	Oryctolagus cuniculus
NCBI Class编号 ncbi_taxonomy_id	9986
宿主生物 host_organism	Oryctolagus cuniculus

Entity 3 Entity 3 polymer

Description description	Mesothelin, cleaved form
Molecular weight formula_weight	1863.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

IPNGYLVLDLSMQEALS

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	742

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8. Citations (1)

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Unit-cell length a length_a	92.960 Å
Unit-cell length b length_b	98.835 Å
Unit-cell length c length_c	66.595 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	131.97 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.520 Å
Low-resolution limit resolution_low	24.760 Å
R factor r_factor	0.1509
R_work r_work	0.1494
R_free r_free	0.1798

fit	/app/data/saxs_computation/p4/9p4c/9p4c.fit
pddf	/app/data/pr_computation/p4/9p4c/9p4c.pr.out
profile	/app/data/saxs_computation/p4/9p4c/9p4c.dat

Crystal structure of Mesothelin C-terminal peptide-RO4 Fab complex

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

Mesothelin, cleaved form

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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)