8CXC | pdb_00008cxc

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/pdb8CXC/pdb

Classification: ANTITUMOR PROTEIN
Organism(s): Mus musculus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-05-20 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: 4.31 Å
R-Value Free:
0.300 (Depositor), 0.289 (DCC)
R-Value Work:
0.243 (Depositor), 0.240 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 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: 108.47 kDa
Atom Count: 6,984
Modeled Residue Count: 938
Deposited Residue Count: 992
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3F2 Antibody light chain	A [auth L]	213	Mus musculus	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3F2 Antibody heavy chain	B [auth H]	218	Mus musculus	Mutation(s): 0

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| 3D Structure

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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv Amatuximab	D [auth A]	234	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.31 Å
R-Value Free: 0.300 (Depositor), 0.289 (DCC)
R-Value Work: 0.243 (Depositor), 0.240 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.303	α = 90
b = 204.175	β = 90
c = 123.114	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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Entry History

& Funding Information

Deposition Data

Released Date: 2023-06-07

Deposition Author(s):

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 2.0: 2024-05-01
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2024-10-30
Changes: Structure summary