1IC5

CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD99A)-HEN LYSOZYME COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural evidence for entropic contribution of salt bridge formation to a protein antigen-antibody interaction: the case of hen lysozyme-HyHEL-10 Fv complex.

Shiroishi, M.Yokota, A.Tsumoto, K.Kondo, H.Nishimiya, Y.Horii, K.Matsushima, M.Ogasahara, K.Yutani, K.Kumagai, I.

(2001) J.Biol.Chem. 276: 23042-23050

  • DOI: 10.1074/jbc.M100480200
  • Primary Citation of Related Structures:  1IC4, 1IC7

  • PubMed Abstract: 
  • A structural and thermodynamic study of the entropic contribution of salt bridge formation to the interaction between hen egg white lysozyme (HEL) and the variable domain fragment (Fv) of anti-HEL antibody, HyHEL-10, was carried out. Three Fv mutants ...

    A structural and thermodynamic study of the entropic contribution of salt bridge formation to the interaction between hen egg white lysozyme (HEL) and the variable domain fragment (Fv) of anti-HEL antibody, HyHEL-10, was carried out. Three Fv mutants (HD32A, HD96A, and HD32AD96A) were prepared, and the interactions between the mutant Fvs and HEL were investigated. Crystallography revealed that the overall structures of these mutant complexes were almost identical to that of wild-type Fv. Little structural changes were observed in the HD32AD96A mutant-HEL complex, and two water molecules were introduced into the mutation site, indicating that the two water molecules structurally compensated for the complete removal of the salt bridges. This result suggests that the entropic contribution of the salt bridge originates from dehydration. In the singly mutated complexes, one water molecule was also introduced into the mutated site, bridging the antigen-antibody interface. However, a local structural difference was observed in the HD32A Fv-HEL complex, and conformational changes occurred due to changes in the relative orientation of the heavy chain to the light chain upon complexation in HD96A Fv-HEL complexes. The reduced affinity of these single mutants for the antigen originates from the increase in entropy loss, indicating that these structural changes also introduced an increase in entropy loss. These results suggest that salt bridge formation makes an entropic contribution to the protein antigen-antibody interaction through reduction of entropy loss due to dehydration and structural changes.


    Organizational Affiliation

    Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 07, Aoba-ku, Sendai 980-8579, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME BINDING IG KAPPA CHAIN
L
107Mus musculusGene Names: Gm10881
Find proteins for P01642 (Mus musculus)
Go to UniProtKB:  P01642
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG1 FAB CHAIN H
H
114Mus musculusN/A
Find proteins for P01823 (Mus musculus)
Go to UniProtKB:  P01823
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME C
Y
129Gallus gallusGene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.165 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.001α = 90.00
b = 57.001β = 90.00
c = 238.086γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
DENZOdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-07-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance