PDBsum entry 6o9c

Immune system

PDB id: 6o9c

Contents

Protein chains

279 a.a.

100 a.a.

Ligands

THR-THR-ALA-PRO-PHE-LEU-SER-GLY-LYS

MES ×2

SO4 ×10

PEG ×2

Waters ×43

PDB id:

6o9c

Name:

Immune system

Title:

Crystal structure of hla-a3 01 In complex with a mutant beta-catenin peptide

Structure:

Hla class i histocompatibility antigen, a-3 alpha chain. Chain: a. Fragment: unp residues 25-304. Synonym: mhc class i antigen a 3. Engineered: yes. Beta-2-microglobulin. Chain: b. Engineered: yes. Catenin beta-1.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hla-a, hlaa. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: b2m, cdabp0092, hdcma22p. Gene: ctnnb1, ctnnb, ok/sw-cl.35, pro2286. Expression_system_taxid: 469008

Resolution:

2.45Å R-factor: 0.216 R-free: 0.259

Authors:

M.S.Miller,S.B.Gabelli

Key ref:

M.S.Miller et al. (2019). An engineered antibody fragment targeting mutant β-catenin via major histocompatibility complex I neoantigen presentation. J Biol Chem, 294, 19322-19334. PubMed id: 31690625 DOI: 10.1074/jbc.RA119.010251

Date:

13-Mar-19 Release date: 13-Nov-19

Protein chain

P04439  (1A03_HUMAN) -  HLA class I histocompatibility antigen, A alpha chain from Homo sapiens

Seq: 365 a.a.

Struc: 279 a.a.*

Protein chain

P61769  (B2MG_HUMAN) -  Beta-2-microglobulin from Homo sapiens

Seq: 119 a.a.

Struc: 100 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1074/jbc.RA119.010251

J Biol Chem 294:19322-19334 (2019)

PubMed id: 31690625

An engineered antibody fragment targeting mutant β-catenin via major histocompatibility complex I neoantigen presentation.

M.S.Miller, J.Douglass, M.S.Hwang, A.D.Skora, M.Murphy, N.Papadopoulos, K.W.Kinzler, B.Vogelstein, S.Zhou, S.B.Gabelli.

ABSTRACT

Mutations in CTNNB1, the gene encoding β-catenin, are common in colon and liver cancers, the most frequent mutation affecting Ser-45 in β-catenin. Peptides derived from WT β-catenin have previously been shown to be presented on the cell surface as part of major histocompatibility complex (MHC) class I, suggesting an opportunity for targeting this common driver gene mutation with antibody-based therapies. Here, crystal structures of both the WT and S45F mutant peptide bound to HLA-A*03:01 at 2.20 and 2.45 Å resolutions, respectively, confirmed the accessibility of the phenylalanine residue for antibody recognition. Phage display was then used to identify single-chain variable fragment clones that selectively bind the S45F mutant peptide presented in HLA-A*03:01 and have minimal WT or other off-target binding. Following the initial characterization of five clones, we selected a single clone, E10, for further investigation. We developed a computational model of the binding of E10 to the mutant peptide-bound HLA-A3, incorporating data from affinity maturation as initial validation. In the future, our model may be used to design clones with maintained specificity and higher affinity. Such derivatives could be adapted into either cell-based (CAR-T) or protein-based (bispecific T-cell engagers) therapies to target cancer cells harboring the S45F mutation in CTNNB1.