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- PDB-9p4c: Crystal structure of Mesothelin C-terminal peptide-RO4 Fab complex -

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Basic information

Entry
Database: PDB / ID: 9p4c
TitleCrystal structure of Mesothelin C-terminal peptide-RO4 Fab complex
Components
  • Heavy chain of the RO4 fab fragment
  • Light chain of the RO4 Fab fragment
  • Mesothelin, cleaved form
KeywordsANTITUMOR PROTEIN / Mesothelin / antibody / IMMUNE SYSTEM
Function / homology
Function and homology information


Post-translational modification: synthesis of GPI-anchored proteins / side of membrane / cell-matrix adhesion / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cell adhesion / endoplasmic reticulum lumen / cell surface / Golgi apparatus / extracellular region ...Post-translational modification: synthesis of GPI-anchored proteins / side of membrane / cell-matrix adhesion / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cell adhesion / endoplasmic reticulum lumen / cell surface / Golgi apparatus / extracellular region / membrane / plasma membrane
Similarity search - Function
Mesothelin / Stereocilin-related / Mesothelin
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsZhan, J. / Maslanka, C. / Xia, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Antib Ther / Year: 2025
Title: Structural analysis of monoclonal antibody RO4 with mesothelin C-terminal peptide
Authors: Zhan, J. / Xia, D.
History
DepositionJun 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Light chain of the RO4 Fab fragment
H: Heavy chain of the RO4 fab fragment
M: Mesothelin, cleaved form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3544
Polymers46,2623
Non-polymers921
Water13,367742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-30 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.960, 98.835, 66.595
Angle α, β, γ (deg.)90.000, 131.972, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Antibody Light chain of the RO4 Fab fragment


Mass: 22506.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit)
#2: Antibody Heavy chain of the RO4 fab fragment


Mass: 21892.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit)
#3: Protein/peptide Mesothelin, cleaved form


Mass: 1863.138 Da / Num. of mol.: 1 / Fragment: C-terminal peptide (UNP residues 590-606) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13421
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 742 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris, pH 6.5 and 16% PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 64882 / % possible obs: 94.3 % / Redundancy: 5.6 % / Biso Wilson estimate: 14.32 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.036 / Net I/σ(I): 19
Reflection shellResolution: 1.52→1.57 Å / Num. unique obs: 4826 / CC1/2: 0.789 / Rpim(I) all: 0.234

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→24.76 Å / SU ML: 0.1491 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.1424
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1798 3262 5.03 %
Rwork0.1494 61547 -
obs0.1509 64809 94.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.07 Å2
Refinement stepCycle: LAST / Resolution: 1.52→24.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 0 6 742 3986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00863311
X-RAY DIFFRACTIONf_angle_d1.06684532
X-RAY DIFFRACTIONf_chiral_restr0.0618552
X-RAY DIFFRACTIONf_plane_restr0.0085572
X-RAY DIFFRACTIONf_dihedral_angle_d12.09031145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.540.30691100.25481677X-RAY DIFFRACTION59.95
1.54-1.570.24741120.2242072X-RAY DIFFRACTION73.66
1.57-1.590.28611340.22722534X-RAY DIFFRACTION88.52
1.59-1.620.24941420.19952566X-RAY DIFFRACTION91.24
1.62-1.650.24061510.18282656X-RAY DIFFRACTION94.35
1.65-1.680.19051210.17772741X-RAY DIFFRACTION95.94
1.68-1.710.2011560.17232706X-RAY DIFFRACTION96.17
1.71-1.750.22731490.16882728X-RAY DIFFRACTION96.29
1.75-1.790.19131340.16182754X-RAY DIFFRACTION96.33
1.79-1.840.18621630.15462726X-RAY DIFFRACTION96.72
1.84-1.890.19291350.14842763X-RAY DIFFRACTION96.79
1.89-1.940.19791250.14772768X-RAY DIFFRACTION97.24
1.94-20.15931590.1392731X-RAY DIFFRACTION97.11
2-2.080.20841390.13872765X-RAY DIFFRACTION97.38
2.08-2.160.1731410.14012791X-RAY DIFFRACTION97.57
2.16-2.260.14851620.13772783X-RAY DIFFRACTION98.26
2.26-2.380.18791420.1382765X-RAY DIFFRACTION97.98
2.38-2.520.20871200.14732842X-RAY DIFFRACTION98.73
2.52-2.720.16421560.14972799X-RAY DIFFRACTION98.7
2.72-2.990.20221350.1492839X-RAY DIFFRACTION98.9
2.99-3.420.17531450.14152824X-RAY DIFFRACTION99.13
3.42-4.310.15021490.13192859X-RAY DIFFRACTION99.37
4.31-24.760.14711820.14532858X-RAY DIFFRACTION99.35

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