7U8C | pdb_00007u8c

Crystal structure of Mesothelin C-terminal peptide-MORAb 15B6 FAB complex

• PDB DOI: https://doi.org/10.2210/pdb7U8C/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Mus musculus
• Mutation(s): No 


• Deposited: 2022-03-08 Released: 2022-06-08 
• Deposition Author(s): Zhan, J., Esser, L., 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: 1.74 Å
• R-Value Free: 
  0.238 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Highly active CAR T cells that bind to a juxtamembrane region of mesothelin and are not blocked by shed mesothelin.

Liu, X., Onda, M., Watson, N., Hassan, R., Ho, M., Bera, T.K., Wei, J., Chakraborty, A., Beers, R., Zhou, Q., Shajahan, A., Azadi, P., Zhan, J., Xia, D., Pastan, I.

(2022) Proc Natl Acad Sci U S A 119: e2202439119-e2202439119

• PubMed: 35512094 
• DOI: https://doi.org/10.1073/pnas.2202439119
• Primary Citation Related Structures: 
  7U8C


• PubMed Abstract: 
  

  SignificanceMesothelin (MSLN) is a cell-surface protein that is a popular target for antibody-based therapies. We have identified shed MSLN as a major obstacle to successful antibody therapies and prepared a monoclonal antibody that inhibits shedding and makes very active CAR T cells whose activity is not blocked by shed MSLN and merits further preclinical development.

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Organizational Affiliation: 
• Laboratory of Molecular Biology, National Cancer Institute (NCI), Bethesda, MD 20892-4264.
Thoracic and GI Malignancies Branch, NCI, Bethesda, MD 20892.
Analytical Services and Training, University of Georgia, Athens, GA 30602-4712.
Laboratory of Cell Biology, NCI, Bethesda, MD 20892-4255.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content 

• Total Structure Weight: 47.53 kDa 
• Atom Count: 3,633 
• Modeled Residue Count: 442 
• Deposited Residue Count: 444 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mesothelin, cleaved form	A [auth BA2]	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MORab 15B6 Fab heavy chain	B [auth H]	214	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MORab 15B6 Fab light chain	C [auth L]	213	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.238 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.832	α = 90
b = 64.832	β = 90
c = 250.134	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
BALBES	phasing
HKL-2000	data collection

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Zhan, J., Esser, L., 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: 2022-06-08
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary