Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.73 kDa 
• Atom Count: 3087 
• Residue Count: 350 
• Unique protein chains: 3

2DQD

Crystal structure of hyhel-10 FV mutant (Hy50f) complexed with hen egg lysozyme

• DOI: 10.2210/pdb2DQD/pdb

• Classification: IMMUNE SYSTEM/HYDROLASE
• Organism(s): Mus musculus, Gallus gallus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-05-25 Released: 2007-01-23 
• Deposition Author(s): Shiroishi, M., Kondo, H., Tsumoto, K., Kumagai, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.215 
• R-Value Work: 0.186 
• R-Value Observed: 0.186 

Literature

Structural consequences of mutations in interfacial Tyr residues of a protein antigen-antibody complex. The case of HyHEL-10-HEL

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

(2007) J Biol Chem 282: 6783-6791

• PubMed: 17166830 
• DOI: 10.1074/jbc.M605197200
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Tyrosine is an important amino acid in protein-protein interaction hot spots. In particular, many Tyr residues are located in the antigen-binding sites of antibodies and endow high affinity and high specificity to these antibodies. To investigate the role of interfacial Tyr residues in protein-protein interactions, we performed crystallographic studies and thermodynamic analyses of the interaction between hen egg lysozyme (HEL) and the anti-HEL antibody HyHEL-10 Fv fragment. HyHEL-10 has six Tyr residues in its antigen-binding site, which were systematically mutated to Phe and Ala using site-directed mutagenesis. The crystal structures revealed several critical roles for these Tyr residues in the interaction between HEL and HyHEL-10 as follows: 1) the aromatic ring of Tyr-50 in the light chain (LTyr-50) was important for the correct ternary structure of variable regions of the immunoglobulin light chain and heavy chain and of HEL; 2) deletion of the hydroxyl group of Tyr-50 in the heavy chain (HTyr-50) resulted in structural changes in the antigen-antibody interface; and 3) the side chains of HTyr-33 and HTyr-53 may help induce fitting of the antibody to the antigen. Hot spot Tyr residues may contribute to the high affinity and high specificity of the antigen-antibody interaction through a diverse set of structural and thermodynamic interactions.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
lysozyme binding Ig kappa chain V23-J2 region	L	107	Mus musculus	Mutation(s): 0  Gene Names: Igkv5-39, Gm1409
Find proteins for Q65ZI1 (Mus musculus) Go to UniProtKB:  Q65ZI1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Ig VH,anti-lysozyme	H	114	Mus musculus	Mutation(s): 0
Find proteins for P01823 (Mus musculus) Go to UniProtKB:  P01823

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Lysozyme C	Y	129	Gallus gallus	Mutation(s): 0  Gene Names: LYZ EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus) Go to UniProtKB:  P00698

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.215 
• R-Value Work: 0.186 
• R-Value Observed: 0.186 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.24	α = 90
b = 56.24	β = 90
c = 232.71	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-05-25 
• Released Date: 2007-01-23 
Deposition Author(s): Shiroishi, M., Kondo, H., Tsumoto, K., Kumagai, I.

Revision History 

• Version 1.0: 2007-01-23
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance