5DFW

CRYSTAL STRUCTURE OF HUMAN CD81 LARGE EXTRACELLULAR LOOP IN COMPLEX WITH SINGLE CHAIN FV FRAGMENT K13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

VH-VL orientation prediction for antibody humanization candidate selection: A case study.

Bujotzek, A.Lipsmeier, F.Harris, S.F.Benz, J.Kuglstatter, A.Georges, G.

(2016) Mabs 8: 288-305

  • DOI: 10.1080/19420862.2015.1117720
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Antibody humanization describes the procedure of grafting a non-human antibody's complementarity-determining regions, i.e., the variable loop regions that mediate specific interactions with the antigen, onto a β-sheet framework that is representative ...

    Antibody humanization describes the procedure of grafting a non-human antibody's complementarity-determining regions, i.e., the variable loop regions that mediate specific interactions with the antigen, onto a β-sheet framework that is representative of the human variable region germline repertoire, thus reducing the number of potentially antigenic epitopes that might trigger an anti-antibody response. The selection criterion for the so-called acceptor frameworks (one for the heavy and one for the light chain variable region) is traditionally based on sequence similarity. Here, we propose a novel approach that selects acceptor frameworks such that the relative orientation of the 2 variable domains in 3D space, and thereby the geometry of the antigen-binding site, is conserved throughout the process of humanization. The methodology relies on a machine learning-based predictor of antibody variable domain orientation that has recently been shown to improve the quality of antibody homology models. Using data from 3 humanization campaigns, we demonstrate that preselecting humanization variants based on the predicted difference in variable domain orientation with regard to the original antibody leads to subsets of variants with a significant improvement in binding affinity.


    Organizational Affiliation

    a Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Penzberg , Nonnenwald 2, Penzberg , Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CD81 antigen
A
98Homo sapiensMutation(s): 0 
Gene Names: CD81 (TAPA1, TSPAN28)
Find proteins for P60033 (Homo sapiens)
Go to Gene View: CD81
Go to UniProtKB:  P60033
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SINGLE CHAIN FV FRAGMENT
H
243N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.190 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 49.652α = 90.00
b = 49.671β = 105.30
c = 80.452γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
DENZOdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-03-02
    Type: Database references