3WLW

Molecular Architecture of the ErbB2 Extracellular Domain Homodimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report



Literature

Molecular architecture of the ErbB2 extracellular domain homodimer.

Hu, S.Sun, Y.Meng, Y.Wang, X.Yang, W.Fu, W.Guo, H.Qian, W.Hou, S.Li, B.Rao, Z.Lou, Z.Guo, Y.

(2015) Oncotarget 6: 1695-1706

  • DOI: 10.18632/oncotarget.2713
  • Primary Citation of Related Structures:  
    3WLW

  • PubMed Abstract: 
  • Human epidermal growth factor receptors (HERs or ErbBs) play crucial roles in numerous cellular processes. ErbB2 is a key member of ErbB family, and its overexpression is recognized as a frequent molecular abnormality. In cancer, this overexpression ...

    Human epidermal growth factor receptors (HERs or ErbBs) play crucial roles in numerous cellular processes. ErbB2 is a key member of ErbB family, and its overexpression is recognized as a frequent molecular abnormality. In cancer, this overexpression correlates with aggressive disease and poor patient outcomes. Dimer-dependent phosphorylation is a key event for the signal transduction of ErbBs. However, the molecular mechanism of the dimerization of ErbB2 remains elusive. In the present work, we report the homodimer architecture of the ErbB2 extracellular domain (ECD) which is unique compared with other dimer-models of ErbBs. The structure of the ErbB2 ECD homodimer represents a "back to head" interaction, in which a protruding β-hairpin arm in domain II of one ErbB2 protomer is inserted into a C-shaped pocket created by domains I-III of the adjacent ErbB2 protomer. This dimerized architecture and its impact on the phosphorylation of ErbB2 intracellular domain were further verified by a mutagenesis study. We also elucidated the different impacts of two clinically administered therapeutic antibodies, trastuzumab and pertuzumab, on ErbB2 dimerization. This information not only provides an understanding of the molecular mechanism of ErbBs dimerization but also elucidates ErbB2-targeted therapy at the molecular level.


    Organizational Affiliation

    School of Pharmacy, Liaocheng University, Liaocheng, Shandong, 252000, P.R. China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor tyrosine-protein kinase erbB-2AB564Homo sapiensMutation(s): 0 
Gene Names: ERBB2HER2MLN19NEUNGL
EC: 2.7.10.1
Find proteins for P04626 (Homo sapiens)
Explore P04626 
Go to UniProtKB:  P04626
NIH Common Fund Data Resources
PHAROS  P04626
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody H ChainCH217Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody L ChainDL217Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
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: 3.09 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.716α = 106.89
b = 104.185β = 99.65
c = 116.712γ = 111.12
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary