Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 235.73 kDa 
• Atom Count: 15481 
• Modelled Residue Count: 1995 
• Deposited Residue Count: 2128 
• Unique protein chains: 3

1S78

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

• PDB DOI: 10.2210/pdb1S78/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Cricetulus griseus, Escherichia coli
• Mutation(s): No 


• Deposited: 2004-01-29 Released: 2004-04-27 
• Deposition Author(s): Franklin, M.C., Carey, K.D., Vajdos, F.F., Leahy, D.J., de Vos, A.M., Sliwkowski, M.X.

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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 

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: 15093539 
• DOI: 10.1016/s1535-6108(04)00083-2
• Primary Citation of Related Structures:  
  1S78


• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor protein-tyrosine kinase erbB-2	A, B	624	Homo sapiens	Mutation(s): 0  Gene Names: ERBB2, HER2, NGL, NEU, MLN19 EC: 2.7.1.112 (PDB Primary Data), 2.7.10.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P04626 (Homo sapiens) Explore P04626  Go to UniProtKB:  P04626
PHAROS:  P04626

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pertuzumab Fab light chain	C, E	214	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q7Z3Y4 (Homo sapiens) Explore Q7Z3Y4  Go to UniProtKB:  Q7Z3Y4

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Pertuzumab Fab heavy chain	D, F	226	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D 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
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 5
Molecule	Chains	Chain Length	2D 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
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	L [auth A], M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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 = 139.412	α = 90
b = 139.412	β = 90
c = 356.873	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-01-29 
• Released Date: 2004-04-27 
Deposition Author(s): Franklin, M.C., Carey, K.D., Vajdos, F.F., Leahy, D.J., de Vos, A.M., Sliwkowski, M.X.

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