Biological Assembly 1  

 3D View: Structure | Electron Density

Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.73 kDa 
• Atom Count: 3084 
• Modelled Residue Count: 350 
• Deposited Residue Count: 350 
• Unique protein chains: 3

1J1P

Crystal structure of HyHEL-10 Fv mutant LS91A complexed with hen egg white lysozyme

• DOI: 10.2210/pdb1J1P/pdb

• Classification: IMMUNE SYSTEM/HYDROLASE
• Organism(s): Mus musculus, Gallus gallus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2002-12-13 Released: 2003-01-14 
• Deposition Author(s): Yokota, A., Tsumoto, K., Shiroishi, M., Kondo, H., Kumagai, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.212 
• R-Value Work: 0.191 

Literature

The Role of Hydrogen Bonding via Interfacial Water Molecules in Antigen-Antibody Complexation. THE HyHEL-10-HEL INTERACTION

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

(2003) J Biol Chem 278: 5410-5418

• PubMed: 12444085 
• DOI: 10.1074/jbc.M210182200
• Primary Citation of Related Structures:  
  1J1O, 1J1P, 1J1X


• PubMed Abstract: 
  

To study the role of hydrogen bonding via interfacial water molecules in protein-protein interactions, we examined the interaction between hen egg white lysozyme (HEL) and its HyHEL-10 variable domain fragment (Fv) antibody. We constructed three antibody mutants (l-Y50F, l-S91A, and l-S93A) and investigated the interactions between the mutant Fvs and HEL. Isothermal titration calorimetry indicated that the mutations significantly decreased the negative enthalpy change (8-25 kJ mol(-1)), despite some offset by a favorable entropy change. X-ray crystallography demonstrated that the complexes had nearly identical structures, including the positions of the interfacial water molecules. Taken together, the isothermal titration calorimetric and x-ray crystallographic results indicate that hydrogen bonding via interfacial water enthalpically contributes to the Fv-HEL interaction despite the partial offset because of entropy loss, suggesting that hydrogen bonding stiffens the antigen-antibody complex.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lysozyme binding Ig kappa chain V23-J2 region	A [auth L]	107	Mus musculus	Mutation(s): 1  Gene Names: Gm10881
UniProt
Find proteins for P01642 (Mus musculus) Explore P01642  Go to UniProtKB:  P01642

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.212 
• R-Value Work: 0.191 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.56	α = 90
b = 56.56	β = 90
c = 234.751	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: 2002-12-13 
• Released Date: 2003-01-14 
Deposition Author(s): Yokota, A., Tsumoto, K., Shiroishi, M., Kondo, H., Kumagai, I.

Revision History  

• Version 1.0: 2003-01-14
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance