9F18 | pdb_00009f18

Crystal structure of a first-in-class antibody for alpha-1,6-fucosylated prostate-specific antigen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 
    0.251 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Development of a first-in-class antibody and a specific assay for alpha-1,6-fucosylated prostate-specific antigen.

Halldorsson, S.Hillringhaus, L.Hojer, C.Muranyi, A.Schraeml, M.Lange, M.S.Tabares, G.

(2024) Sci Rep 14: 16512-16512

  • DOI: https://doi.org/10.1038/s41598-024-67545-1
  • Primary Citation Related Structures: 
    9F18, 9F1I

  • PubMed Abstract: 

    Prostate-specific antigen (PSA) levels are widely used to screen for prostate cancer, yet the test has poor sensitivity, specificity and predictive value, which leads to overdiagnosis and overtreatment. Alterations in the glycosylation status of PSA, including fucosylation, may offer scope for an improved biomarker. We sought to generate a monoclonal antibody (mAb) targeting α-1,6-fucosylated PSA (fuc-PSA) and to develop a tissue-based immunological assay for fuc-PSA detection. Immunogens representing fuc-PSA were used for immunisation and resultant mAbs were extensively characterised. The mAbs reacted specifically with fuc-PSA-specific glycopeptide, but not with aglycosylated PSA or glycan without the PSA peptide. Reactivity was confirmed using high-throughput surface plasmon resonance spectroscopy. X-ray crystallography investigations showed that the mAbs bound to an α-helical form of the peptide, whereas the native PSA epitope is linear. Protein unfolding was required for detection of fuc-PSA in patient samples. Peptide inhibition of fuc-PSA mAbs was observed with positive screening reagents, and target epitope specificity was observed in formalin-fixed, paraffin-embedded tissue samples. This research introduces a well-characterised, first-in-class antibody targeting fuc-PSA and presents the first crystal structure of an antibody demonstrating glycosylation-specific binding to a peptide.


  • Organizational Affiliation
    • Pharma Research and Early Development, F. Hoffmann-La Roche AG, Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 93.44 kDa 
  • Atom Count: 6,459 
  • Modeled Residue Count: 880 
  • Deposited Residue Count: 894 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain rabbit fabA [auth H],
B [auth I]
230Oryctolagus cuniculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain rabbit fabC [auth L],
D [auth M]
217Oryctolagus cuniculusMutation(s): 0 

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A [auth H],
B [auth I]
L-PEPTIDE LINKINGC5 H7 N O3GLN

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free:  0.251 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.219α = 90
b = 66.735β = 112.087
c = 91.713γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
F. Hoffmann-La Roche LTDSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary