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 
  • R-Value Observed: 0.227 

wwPDB Validation 3D Report Full Report



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

  • DOI: 10.1016/s1535-6108(04)00083-2
  • Structures With Same Primary Citation

  • 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: 
    • 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
    • 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
    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-2A, B624Homo sapiensMutation(s): 0 
Gene Names: ERBB2, HER2, NGL, NEU, MLN19
EC: 2.7.1.112 (PDB Primary Data), 2.7.10.1 (UniProt)
Find proteins for P04626 (Homo sapiens)
Explore P04626 
Go to UniProtKB:  P04626
NIH Common Fund Data Resources
PHAROS  P04626
GTEx  ENSG00000141736
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pertuzumab Fab light chainC, E214Mus musculusMutation(s): 0 
Find proteins for Q7Z3Y4 (Homo sapiens)
Explore Q7Z3Y4 
Go to UniProtKB:  Q7Z3Y4
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Pertuzumab Fab heavy chainD, F226Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I, K
2 N-Glycosylation
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J
3 N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
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 
  • R-Value Observed: 0.227 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.412α = 90
b = 139.412β = 90
c = 356.873γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary