8GQ1

HyHEL10 Fab complexed with hen egg lysozyme carrying arginine cluster in framework region of light chain.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Arginine cluster introduction on framework region in anti-lysozyme antibody improved association rate constant by changing conformational diversity of CDR loops.

Maeta, S.Nakakido, M.Matsuura, H.Sakai, N.Hirata, K.Kuroda, D.Fukunaga, A.Tsumoto, K.

(2023) Protein Sci 32: e4745-e4745

  • DOI: https://doi.org/10.1002/pro.4745
  • Primary Citation of Related Structures:  
    8GQ1

  • PubMed Abstract: 

    Antibodies are used for many therapeutic and biotechnological purposes. Because the affinity of an antibody to the antigen is critical for clinical efficacy of pharmaceuticals, many affinity maturation strategies have been developed. Although we previously reported an affinity maturation strategy in which the association rate of the antibody toward its antigen is improved by introducing a cluster of arginine residues into the framework region of the antibody, the detailed molecular mechanism responsible for this improvement has been unknown. In this study, we introduced five arginine residues into an anti-hen egg white lysozyme antibody (HyHEL10) Fab fragment to create the R5-mutant and comprehensively characterized the interaction between antibody and antigen using thermodynamic analysis, X-ray crystallography, and molecular dynamics (MD) simulations. Our results indicate that introduction of charged residues strongly enhanced the association rate, as previously reported, and the antibody-antigen complex structure was almost the same for the R5-mutant and wild-type Fabs. The MD simulations indicate that the mutation increased conformational diversity in complementarity-determining region loops and thereby enhanced the association rate. These observations provide the molecular basis of affinity maturation by R5 mutation.


  • Organizational Affiliation

    Bio-Diagnostic Reagent Technology Center, Sysmex Corporation, Kobe, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme CA [auth C]129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light Chain of HyHel10 Antibody Fragment (Fab)B [auth L]214Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy Chain of HyHel10 Antibody Fragment (Fab)C [auth H]231Mus musculusMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
D [auth L]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.9α = 90
b = 147.9β = 90
c = 137.7γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21H05090
Japan Society for the Promotion of Science (JSPS)Japan19H05766
Japan Society for the Promotion of Science (JSPS)Japan20H02531
Japan Agency for Medical Research and Development (AMED)Japan18ak0101100
Japan Agency for Medical Research and Development (AMED)Japan19am0401010
Japan Agency for Medical Research and Development (AMED)Japan20mk0101170

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Structure summary