6O9C

Crystal structure of HLA-A3*01 in complex with a mutant beta-catenin peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report

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This is version 1.4 of the entry. See complete history


Literature

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

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

(2019) J Biol Chem 294: 19322-19334

  • DOI: https://doi.org/10.1074/jbc.RA119.010251
  • Primary Citation of Related Structures:  
    6O9B, 6O9C

  • PubMed 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 .


  • Organizational Affiliation

    GE Healthcare Life Sciences, Marlborough, Massachusetts 01752.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-3 alpha chain300Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04439
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin119Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Catenin beta-19Homo sapiensMutation(s): 1 
Gene Names: CTNNB1CTNNBOK/SW-cl.35PRO2286
UniProt & NIH Common Fund Data Resources
Find proteins for P35222 (Homo sapiens)
Explore P35222 
Go to UniProtKB:  P35222
PHAROS:  P35222
GTEx:  ENSG00000168036 
Entity Groups  
UniProt GroupP35222
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
P [auth B],
Q [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
O [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.123α = 90
b = 155.123β = 90
c = 85.316γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Currently 6O9C does not have a validation slider image.



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP50CA062924
Department of Defense (DOD, United States)United StatesW81XWH-16-1-0486

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-25
    Changes: Database references
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description