8CYH | pdb_00008cyh

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.38 Å
R-Value Free:
0.268 (Depositor), 0.264 (DCC)
R-Value Work:
0.230 (Depositor), 0.227 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13421
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain C [auth M]	Go to GlyGen: Q13421-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth M] SDF format, chain D [auth M] MOL2 format, chain E [auth M] MOL2 format, chain D [auth M] mmCIF format, chain E [auth M] mmCIF format, chain D [auth M]	D [auth M], E [auth M]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth M] Focus chain E [auth M] Interactions & Density Focus chain D [auth M] Focus chain E [auth M]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.38 Å
R-Value Free: 0.268 (Depositor), 0.264 (DCC)
R-Value Work: 0.230 (Depositor), 0.227 (DCC)
R-Value Observed: 0.232 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-06-07

Deposition Author(s):

Bandaranayake, A.D.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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
Version 1.3: 2024-11-13
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.