1S78

Insights into ErbB signaling from the structure of the ErbB2-pertuzumab complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Insights into ErbB signaling from the structure of the ErbB2-pertuzumab complex.

Franklin, M.C.Carey, K.D.Vajdos, F.F.Leahy, D.J.De Vos, A.M.Sliwkowski, M.X.

(2004) Cancer Cell 5: 317-328


  • PubMed Abstract: 
  • We have determined the 3.2 A X-ray crystal structure of the extracellular domain of the human epidermal growth factor receptor 2 (ErbB2 or HER2) in a complex with the antigen binding fragment of pertuzumab, an anti-ErbB2 monoclonal antibody also know ...

    We have determined the 3.2 A X-ray crystal structure of the extracellular domain of the human epidermal growth factor receptor 2 (ErbB2 or HER2) in a complex with the antigen binding fragment of pertuzumab, an anti-ErbB2 monoclonal antibody also known as 2C4 or Omnitarg. Pertuzumab binds to ErbB2 near the center of domain II, sterically blocking a binding pocket necessary for receptor dimerization and signaling. The ErbB2-pertuzumab structure, combined with earlier mutagenesis data, defines the pertuzumab residues essential for ErbB2 interaction. To analyze the ErbB2 side of the interface, we have mutated a number of residues contacting pertuzumab and examined the effects of these mutations on pertuzumab binding and ErbB2-ErbB3 heterodimerization. We have also shown that conserved residues previously shown to be necessary for EGF receptor homodimerization may be dispensible for ErbB2-ErbB3 heterodimerization.


    Related Citations: 
    • Targeting ligand-activated ErbB2 signaling inhibits breast and prostate tumor growth
      Agus, D.B.,Akita, R.W.,Fox, W.D.,Lewis, G.D.,Higgins, B.,Pisacane, P.I.,Lofgren, J.A.,Tindell, C.,Evans, D.P.,Maiese, K.,Scher, H.I.,Sliwkowski, M.X.
      (2002) Cancer Cell 2: 127
    • Structure of the extracellular region of HER2 alone and in complex with the Herceptin Fab
      Cho, H.S.,Mason, K.,Ramyar, K.X.,Stanley, A.M.,Gabelli, S.B.,Denney Jr., D.W.,Leahy, D.J.
      (2003) Nature 421: 756
    • Comprehensive functional maps of the antigen-binding site of an anti-ErbB2 antibody obtained with shotgun scanning mutagenesis
      Vajdos, F.F.,Adams, C.W.,Breece, T.N.,Presta, L.G.,de Vos, A.M.,Sidhu, S.S.
      (2002) J.Mol.Biol. 320: 415


    Organizational Affiliation

    Department of Protein Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94114 USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor protein-tyrosine kinase erbB-2
A, B
624Homo sapiensGene 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
Pertuzumab Fab light chain
C, E
214Homo sapiens
Find proteins for Q7Z3Y4 (Homo sapiens)
Go to UniProtKB:  Q7Z3Y4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Pertuzumab Fab heavy chain
D, F
226N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.224 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 139.412α = 90.00
b = 139.412β = 90.00
c = 356.873γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance