6MY5

Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M,LC-S30bR]

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Cricetulus griseus
  • Mutation(s): No 

  • Deposited: 2018-11-01 Released: 2019-07-31 
  • Deposition Author(s): Shi, R.
  • Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1080/19420862.2019.1632114
  • Primary Citation of Related Structures:  
    6MXR, 6MXS, 6MY4, 6MY5

  • 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 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 ...

    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: 

    Human Health Therapeutics Research Centre, National Research Council Canada , Montreal , QC H4P 2R2 , Canada.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
anti-VEGF-A Fab fragment bH1 heavy chainA [auth H],
C [auth A]		236Homo sapiensMutation(s): 0 
Gene Names: HEL-214
UniProt
Find proteins for V9HW68 (Homo sapiens)
Explore V9HW68 
Go to UniProtKB:  V9HW68
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV9HW68
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
anti-VEGF-A Fab fragment bH1 light chainB [auth L],
D [auth B]		218Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q7Z3Y4 (Homo sapiens)
Explore Q7Z3Y4 
Go to UniProtKB:  Q7Z3Y4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z3Y4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.599α = 90
b = 65.53β = 100.73
c = 92.56γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

  • Released Date: 2019-07-31 
    • Deposition Author(s): Shi, R.
Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada436202

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence