6MY4

Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M,LC-S30bR]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Binding symmetry and surface flexibility mediate antibody self-association.

Schrag, J.D.Picard, M.E.Gaudreault, F.Gagnon, L.P.Baardsnes, J.Manenda, M.S.Sheff, J.Deprez, C.Baptista, C.Hogues, H.Kelly, J.F.Purisima, E.O.Shi, R.Sulea, T.

(2019) Mabs 11: 1300-1318

  • DOI: 10.1080/19420862.2019.1632114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Solution stability is an important factor in the optimization of engineered biotherapeutic candidates such as monoclonal antibodies because of its possible effects on manufacturability, pharmacology, efficacy and safety. A detailed atomic understandi ...

    Solution stability is an important factor in the optimization of engineered biotherapeutic candidates such as monoclonal antibodies because of its possible effects on manufacturability, pharmacology, efficacy and safety. A detailed atomic understanding of the mechanisms governing self-association of natively folded protein monomers is required to devise predictive tools to guide screening and re-engineering along the drug development pipeline. We investigated pairs of affinity-matured full-size antibodies and observed drastically different propensities to aggregate from variants differing by a single amino-acid. Biophysical testing showed that antigen-binding fragments (Fabs) from the aggregating antibodies also reversibly associated with equilibrium dissociation constants in the low-micromolar range. Crystal structures (PDB accession codes 6MXR, 6MXS, 6MY4, 6MY5) and bottom-up hydrogen-exchange mass spectrometry revealed that Fab self-association occurs in a symmetric mode that involves the antigen complementarity-determining regions. Subtle local conformational changes incurred upon point mutation of monomeric variants foster formation of complementary polar interactions and hydrophobic contacts to generate a dimeric Fab interface. Testing of popular in silico tools generally indicated low reliabilities for predicting the aggregation propensities observed. A structure-aggregation data set is provided here in order to stimulate further improvements of in silico tools for prediction of native aggregation. Incorporation of intermolecular docking, conformational flexibility, and short-range packing interactions may all be necessary features of the ideal algorithm.


    Organizational Affiliation

    a Human Health Therapeutics Research Centre , National Research Council Canada , Montreal , QC H4P 2R2 , Canada.,b Département de Biochimie, de Microbiologie et de Bio-informatique, PROTEO, and Institut de Biologie Intégrative et des Systèmes (IBIS) , Université Laval, Pavillon Charles-Eugène-Marchand , Québec City, QC G1V 0A6 , Canada.,c Human Health Therapeutics Research Centre , National Research Council Canada , Ottawa , ON K1A 0R6 , Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
anti-VEGF-A Fab fragment bH1 heavy chain
H, A
236Homo sapiensMutation(s): 0 
Gene Names: HEL-214
Find proteins for V9HW68 (Homo sapiens)
Go to UniProtKB:  V9HW68
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
anti-VEGF-A Fab fragment bH1 light chain
L, B
218Homo sapiensMutation(s): 0 
Find proteins for Q7Z3Y4 (Homo sapiens)
Go to UniProtKB:  Q7Z3Y4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, H, L
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.869α = 90.00
b = 65.860β = 99.93
c = 93.130γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
iMOSFLMdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (Canada)Canada436202

Revision History 

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-09-25
    Type: Data collection, Database references