8CYH

Novel Anti-Mesothelin Antibodies Enable Crystallography of the Intact Mesothelin Ectodo- main and Engineering of Potent, T cell-engaging Bispecific Therapeutics

• PDB DOI: https://doi.org/10.2210/pdb8CYH/pdb

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


• Deposited: 2022-05-23 Released: 2023-06-07 
• Deposition Author(s): Bandaranayake, A.D., Rupert, P.B., Lin, I., Pilat, K., Ruff, R.O., Friend, D.J., Chan, M.K., Clarke, M., Carter, J., Meshinchi, S., Mehlin, C., Olson, J.M., Strong, R.K., Correnti, C.E.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.38 Å
• R-Value Free: 0.268 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

Starting Model: experimental

Literature

Novel mesothelin antibodies enable crystallography of the intact mesothelin ectodomain and engineering of potent, T cell-engaging bispecific therapeutics

Lin, I., Rupert, P.B., Pilat, K., Ruff, R.O., Friend, D.J., Chan, M.K., Clarke, M., Hoffstrom, B.G., Carter, J., Meshinchi, S., Bandaranayake, A.D., Mehlin, C., Olson, J.M., Strong, R.K., Correnti, C.E.

(2023) Front Drug Discov 3

• DOI: https://doi.org/10.3389/fddsv.2023.1216516

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 84.04 kDa 
• Atom Count: 5,244 
• Modelled Residue Count: 717 
• Deposited Residue Count: 763 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A12 antibody light chain	A [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
A12 antibody heavy chain	B [auth H]	222	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mesothelin, cleaved form	C [auth M]	327	Homo sapiens	Mutation(s): 0  Gene Names: MSLN, MPF
UniProt & NIH Common Fund Data Resources
Find proteins for Q13421 (Homo sapiens) Explore Q13421  Go to UniProtKB:  Q13421
PHAROS:  Q13421 GTEx:  ENSG00000102854
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q13421-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth M], E [auth M]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.38 Å
• R-Value Free: 0.268 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.112	α = 90
b = 124.862	β = 90
c = 302.748	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-07 
Deposition Author(s): Bandaranayake, A.D., Rupert, P.B., Lin, I., Pilat, K., Ruff, R.O., Friend, D.J., Chan, M.K., Clarke, M., Carter, J., Meshinchi, S., Mehlin, C., Olson, J.M., Strong, R.K., Correnti, C.E.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-06-07
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2023-12-20
  Changes: Database references