9P4C | pdb_00009p4c

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

• PDB DOI: https://doi.org/10.2210/pdb9P4C/pdb

• Classification: ANTITUMOR PROTEIN
• Organism(s): Oryctolagus cuniculus, Homo sapiens
• Expression System: Oryctolagus cuniculus
• Mutation(s): No 


• Deposited: 2025-06-16 Released: 2025-11-12 
• Deposition Author(s): Zhan, J., Maslanka, C., Xia, D.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

RO4, a high-affinity humanized antibody against the juxtamembrane region of mesothelin for targeted cancer therapy.

Onda, M., Liu, X., Liu, W., Zhan, J., Maslanka, C.A., Xia, D., Ho, M., Pastan, I.

(2026) Antib Ther 9: 1-12

• PubMed: 41550974 
• DOI: https://doi.org/10.1093/abt/tbaf022
• Primary Citation Related Structures: 
  9P4C


• PubMed Abstract: 
  

  Mesothelin (MSLN) is a surface antigen highly expressed in several solid tumors, including mesothelioma, ovarian, and pancreatic cancers. However, therapeutic efficacy of MSLN-targeted agents is often compromised by shed MSLN (SM), which acts as a soluble decoy and accumulates in tumor microenvironments, reducing antibody engagement at the tumor surface. To overcome this barrier, we generated antibodies targeting the membrane-proximal, non-shed region of MSLN using a peptide encompassing major cleavage sites for rabbit immunization. From 200 B-cell clones, 14 antibodies specific to the juxtamembrane region of MSLN were identified. The lead candidate, RO4, underwent detailed characterization and humanization to improve clinical applicability. Humanized RO4 (hRO4) exhibited enhanced binding affinity to MSLN and specifically recognized tumor-associated, non-shed epitopes. Structural analysis confirmed precise epitope engagement near the cleavage site. hRO4 effectively inhibited mesothelin shedding in vitro and enabled potent tumor eradication when expressed in chimeric antigen receptor (CAR) T cells in NOD scid gamma mouse models. Targeting a non-shed epitope of MSLN with hRO4 overcomes a critical limitation of conventional MSLN-directed therapies. By avoiding decoy interference and enhancing tumor-specific targeting, hRO4-based therapeutics offer promising clinical potential for improving outcomes in MSLN-positive cancers.

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Organizational Affiliation: 
• Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States.
Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.35 kDa 
• Atom Count: 3,986 
• Modeled Residue Count: 444 
• Deposited Residue Count: 444 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of the RO4 Fab fragment	A [auth L]	216	Oryctolagus cuniculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of the RO4 fab fragment	B [auth H]	211	Oryctolagus cuniculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mesothelin, cleaved form	C [auth M]	17	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q13421 (Homo sapiens) Explore Q13421  Go to UniProtKB:  Q13421
PHAROS:  Q13421 GTEx:  ENSG00000102854

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	B [auth H]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.96	α = 90
b = 98.835	β = 131.972
c = 66.595	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
BALBES	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Zhan, J., Maslanka, C., Xia, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release
  
• Version 1.1: 2026-02-04
  Changes: Database references