3WII

Crystal structure of the Fab fragment of B2212A, a murine monoclonal antibody specific for the third fibronectin domain (Fn3) of human ROBO1.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses

Nakayama, T.Mizohata, E.Yamashita, T.Nagatoishi, S.Nakakido, M.Iwanari, H.Mochizuki, Y.Kado, Y.Yokota, Y.Satoh, R.Tsumoto, K.Fujitani, H.Kodama, T.Hamakubo, T.Inoue, T.

(2015) Protein Sci. 24: 328-340

  • DOI: 10.1002/pro.2619
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ROBO1, fibronectin Type-III domain (Fn)-containing protein, is a novel immunotherapeutic target for hepatocellular carcinoma in humans. The crystal structure of the antigen-binding fragment (Fab) of B2212A, the monoclonal antibody against the third F ...

    ROBO1, fibronectin Type-III domain (Fn)-containing protein, is a novel immunotherapeutic target for hepatocellular carcinoma in humans. The crystal structure of the antigen-binding fragment (Fab) of B2212A, the monoclonal antibody against the third Fn domain (Fn3) of ROBO1, was determined in pursuit of antibody drug for hepatocellular carcinoma. This effort was conducted in the presence or absence of the antigen, with the chemical features being investigated by determining the affinity of the antibody using molecular dynamics (MD) and thermodynamics. The structural comparison of B2212A Fab between the complex and the free form revealed that the interfacial Tyr(L) 50 (superscripts L, H, and F stand for the residues in the light chain, heavy chain, and Fn3, respectively) played important roles in Fn3 recognition. That is, the aromatic ring of Tyr(L) 50 pivoted toward Phe(F) 68, forming a CH/π interaction and a new hydrogen bond with the carbonyl O atom of Phe(F) 68. MD simulations predicted that the Tyr(L) 50-Phe(F) 68 interaction almost entirely dominated Fab-Fn3 binding, and Ala-substitution of Tyr(L) 50 led to a reduced binding of the resultant complex. On the contrary, isothermal titration calorimetry experiments underscored that Ala-substitution of Tyr(L) 50 caused an increase of the binding enthalpy between B2212A and Fn3, but importantly, it induced an increase of the binding entropy, resulting in a suppression of loss in the Gibbs free energy in total. These results suggest that mutation analysis considering the binding entropy as well as the binding enthalpy will aid in the development of novel antibody drugs for hepatocellular carcinoma.


    Organizational Affiliation

    Structural Physical Chemistry, Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
anti-human ROBO1 antibody B2212A Fab light chain
L, M
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
anti-human ROBO1 antibody B2212A Fab heavy chain
H, I
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.823α = 90.00
b = 136.490β = 91.86
c = 77.512γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
HKL-2000data reduction
MOLREPphasing
PHENIXrefinement
HKL-2000data scaling
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
BBSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-03-04
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description