7PKL | pdb_00007pkl

Mechanistic understanding of antibody masking with anti-idiotypic antibody fragments


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.265 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Mechanistic insights into the rational design of masked antibodies.

Orozco, C.T.Bersellini, M.Irving, L.M.Howard, W.W.Hargreaves, D.Devine, P.W.A.Siouve, E.Browne, G.J.Bond, N.J.Phillips, J.J.Ravn, P.Jackson, S.E.

(null) MAbs 14: 2095701-2095701

  • DOI: https://doi.org/10.1080/19420862.2022.2095701
  • Primary Citation Related Structures: 
    7PKL

  • PubMed Abstract: 

    Although monoclonal antibodies have greatly improved cancer therapy, they can trigger side effects due to on-target, off-tumor toxicity. Over the past decade, strategies have emerged to successfully mask the antigen-binding site of antibodies, such that they are only activated at the relevant site, for example, after proteolytic cleavage. However, the methods for designing an ideal affinity-based mask and what parameters are important are not yet well understood. Here, we undertook mechanistic studies using three masks with different properties and identified four critical factors: binding site and affinity, as well as association and dissociation rate constants, which also played an important role. HDX-MS was used to identify the location of binding sites on the antibody, which were subsequently validated by obtaining a high-resolution crystal structure for one of the mask-antibody complexes. These findings will inform future designs of optimal affinity-based masks for antibodies and other therapeutic proteins.


  • Organizational Affiliation
    • Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.

Macromolecule Content 

  • Total Structure Weight: 64.24 kDa 
  • Atom Count: 4,497 
  • Modeled Residue Count: 556 
  • Deposited Residue Count: 594 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
trastuzumab Heavy ChainA [auth H]226Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
trastuzumab Light Chain VHH fusionB [auth L]368Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.265 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.742α = 90
b = 59.965β = 90
c = 63.499γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary