Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer -A2B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38751.89 
• Atom Count: 2721 
• Residue Count: 350 
• Unique protein chains: 3

3A6C

Crystal Structure of HyHEL-10 Fv mutant LN92D complexed with hen egg white lysozyme

• DOI: 10.2210/pdb3A6C/pdb

• Classification: IMMUNE SYSTEM/HYDROLASE
• Organism(s): Gallus gallus
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2009-08-28 Released: 2009-12-22 
• Deposition Author(s): Yokota, A., Tsumoto, K., Shiroishi, M., Nakanishi, T., Kondo, H., Kumagai, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.216 
• R-Value Work: 0.186 

Literature

Contribution of asparagine residues to the stabilization of a proteinaceous antigen-antibody complex, HyHEL-10-hen egg white lysozyme

Yokota, A., Tsumoto, K., Shiroishi, M., Nakanishi, T., Kondo, H., Kumagai, I.

(2010) J.Biol.Chem. 285: 7686-7696

• PubMed: 20038580 
• DOI: 10.1074/jbc.M109.089623
• Primary Citation of Related Structures:  
  3A6B, 3A67


• PubMed Abstract: 
  

Many germ line antibodies have asparagine residues at specific sites to achieve specific antigen recognition. To study the role of asparagine residues in the stabilization of antigen-antibody complexes, we examined the interaction between hen egg white lysozyme (HEL) and the corresponding HyHEL-10 variable domain fragment (Fv). We introduced Ala and Asp substitutions into the Fv side chains of L-Asn-31, L-Asn-32, and L-Asn-92, which interact directly with residues in HEL via hydrogen bonding in the wild-type Fv-HEL complex, and we investigated the interactions between these mutant antibodies and HEL. Isothermal titration calorimetric analysis showed that all the mutations decreased the negative enthalpy change and decreased the association constants of the interaction. Structural analyses showed that the effects of the mutations on the structure of the complex could be compensated for by conformational changes and/or by gains in other interactions. Consequently, the contribution of two hydrogen bonds was minor, and their abolition by mutation resulted in only a slight decrease in the affinity of the antibody for its antigen. By comparison, the other two hydrogen bonds buried at the interfacial area had large enthalpic advantage, despite entropic loss that was perhaps due to stiffening of the interface by the bonds, and were crucial to the strength of the interaction. Deletion of these strong hydrogen bonds could not be compensated for by other structural changes. Our results suggest that asparagine can provide the two functional groups for strong hydrogen bond formation, and their contribution to the antigen-antibody interaction can be attributed to their limited flexibility and accessibility at the complex interface.

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Organizational Affiliation: 

Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 6-6-11, Sendai 980-8579, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysozyme binding ig kappa chain V23-J2 region	L	107	N/A
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
IG VH, anti-lysozyme	H	114	N/A
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Lysozyme C	Y	129	Gallus gallus	Gene 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: 1.8 Å
• R-Value Free: 0.216 
• R-Value Work: 0.186 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 56.573	α = 90.00
b = 56.573	β = 90.00
c = 233.679	γ = 90.00

Software Package:

Software Name	Purpose
SCALA	data scaling
MOSFLM	data reduction
CNS	phasing
ADSC	data collection
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-08-28 
• Released Date: 2009-12-22 
• Deposition Author(s): Yokota, A., Tsumoto, K., Shiroishi, M., Nakanishi, T., Kondo, H., Kumagai, I.

Revision History 

• Version 1.0: 2009-12-22
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance