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)

---

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

Structural analysis of monoclonal antibody RO4 with mesothelin C-terminal peptide

Zhan, J., Xia, D.

(2025) Antib Ther 

• DOI: https://doi.org/10.1093/abt/tbaf022

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.

---

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