3BE1

Dual specific bH1 Fab in complex with the extracellular domain of HER2/ErbB-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Variants of the antibody herceptin that interact with HER2 and VEGF at the antigen binding site

Bostrom, J.Yu, S.F.Kan, D.Appleton, B.A.Lee, C.V.Billeci, K.Man, W.Peale, F.Ross, S.Wiesmann, C.Fuh, G.

(2009) Science 323: 1610-1614

  • DOI: 10.1126/science.1165480
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The interface between antibody and antigen is often depicted as a lock and key, suggesting that an antibody surface can accommodate only one antigen. Here, we describe an antibody with an antigen binding site that binds two distinct proteins with hig ...

    The interface between antibody and antigen is often depicted as a lock and key, suggesting that an antibody surface can accommodate only one antigen. Here, we describe an antibody with an antigen binding site that binds two distinct proteins with high affinity. We isolated a variant of Herceptin, a therapeutic monoclonal antibody that binds the human epidermal growth factor receptor 2 (HER2), on the basis of its ability to simultaneously interact with vascular endothelial growth factor (VEGF). Crystallographic and mutagenesis studies revealed that distinct amino acids of this antibody, called bH1, engage HER2 and VEGF energetically, but there is extensive overlap between the antibody surface areas contacting the two antigens. An affinity-improved version of bH1 inhibits both HER2- and VEGF-mediated cell proliferation in vitro and tumor progression in mouse models. Such "two-in-one" antibodies challenge the monoclonal antibody paradigm of one binding site, one antigen. They could also provide new opportunities for antibody-based therapy.


    Organizational Affiliation

    Department of Protein Engineering, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor tyrosine-protein kinase erbB-2
A
624Homo sapiensMutation(s): 0 
Gene Names: ERBB2 (HER2, MLN19, NEU, NGL)
EC: 2.7.10.1
Find proteins for P04626 (Homo sapiens)
Go to Gene View: ERBB2
Go to UniProtKB:  P04626
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab Fragment-Heavy Chain
H
230N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab Fragment-Light Chain
L
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
L
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.324α = 90.00
b = 115.056β = 90.00
c = 208.171γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing
REFMACrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description