Biological Assembly 1  

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

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.

Macromolecule Content

• Total Structure Weight: 107.84 kDa 
• Atom Count: 7475 
• Modelled Residue Count: 988 
• Deposited Residue Count: 997 
• Unique protein chains: 3

3WSQ

Structure of HER2 with an Fab

• PDB DOI: 10.2210/pdb3WSQ/pdb

• Classification: TRANSFERASE/IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2014-03-20 Released: 2015-03-25 
• Deposition Author(s): Fu, W.Y., Wang, Y.X., Zhou, L.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.258 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 

Literature

Insights into HER2 signaling from step-by-step optimization of anti-HER2 antibodies.

Fu, W., Wang, Y., Zhang, Y., Xiong, L., Takeda, H., Ding, L., Xu, Q., He, L., Tan, W., Bethune, A.N., Zhou, L.

(2014) MAbs 6: 978-990

• PubMed: 24838231 
• DOI: 10.4161/mabs.28786
• Primary Citation of Related Structures:  
  3WSQ


• PubMed Abstract: 
  

HER2, a ligand-free tyrosine kinase receptor of the HER family, is frequently overexpressed in breast cancer. The anti-HER2 antibody trastuzumab has shown significant clinical benefits in metastatic breast cancer; however, resistance to trastuzumab is common. The development of monoclonal antibodies that have complementary mechanisms of action results in a more comprehensive blockade of ErbB2 signaling, especially HER2/HER3 signaling. Use of such antibodies may have clinical benefits if these antibodies can become widely accepted. Here, we describe a novel anti-HER2 antibody, hHERmAb-F0178C1, which was isolated from a screen of a phage display library. A step-by-step optimization method was employed to maximize the inhibitory effect of this anti-HER2 antibody. Crystallographic analysis was used to determine the three-dimensional structure to 3.5 Å resolution, confirming that the epitope of this antibody is in domain III of HER2. Moreover, this novel anti-HER2 antibody exhibits superior efficacy in blocking HER2/HER3 heterodimerization and signaling, and its use in combination with pertuzumab has a synergistic effect. Characterization of this antibody revealed the important role of a ligand binding site within domain III of HER2. The results of this study clearly indicate the unique potential of hHERmAb-F0178C1, and its complementary inhibition effect on HER2/HER3 signaling warrants its consideration as a promising clinical treatment.

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Organizational Affiliation: 

Central Laboratory; Navy General Hospital; Beijing, PR China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-2	A	564	Homo sapiens	Mutation(s): 0  Gene Names: ERBB2, HER2, MLN19, NEU, NGL EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04626 (Homo sapiens) Explore P04626  Go to UniProtKB:  P04626
PHAROS:  P04626 GTEx:  ENSG00000141736

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Light Chain	B [auth L]	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Heavy Chain	C [auth H]	218	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.258 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.562	α = 90
b = 82.46	β = 90.91
c = 110.339	γ = 90

Software Package:

Software Name	Purpose
bioteX	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-03-20 
• Released Date: 2015-03-25 
Deposition Author(s): Fu, W.Y., Wang, Y.X., Zhou, L.J.

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description