4P59

HER3 extracellular domain in complex with Fab fragment of MOR09825


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

An antibody that locks HER3 in the inactive conformation inhibits tumor growth driven by HER2 or neuregulin.

Garner, A.P.Bialucha, C.U.Sprague, E.R.Garrett, J.T.Sheng, Q.Li, S.Sineshchekova, O.Saxena, P.Sutton, C.R.Chen, D.Chen, Y.Wang, H.Liang, J.Das, R.Mosher, R.Gu, J.Huang, A.Haubst, N.Zehetmeier, C.Haberl, M.Elis, W.Kunz, C.Heidt, A.B.Herlihy, K.Murtie, J.Schuller, A.Arteaga, C.L.Sellers, W.R.Ettenberg, S.A.

(2013) Cancer Res 73: 6024-6035

  • DOI: https://doi.org/10.1158/0008-5472.CAN-13-1198
  • Primary Citation of Related Structures:  
    4P59

  • PubMed Abstract: 

    HER2/HER3 dimerization resulting from overexpression of HER2 or neuregulin (NRG1) in cancer leads to HER3-mediated oncogenic activation of phosphoinositide 3-kinase (PI3K) signaling. Although ligand-blocking HER3 antibodies inhibit NRG1-driven tumor growth, they are ineffective against HER2-driven tumor growth because HER2 activates HER3 in a ligand-independent manner. In this study, we describe a novel HER3 monoclonal antibody (LJM716) that can neutralize multiple modes of HER3 activation, making it a superior candidate for clinical translation as a therapeutic candidate. LJM716 was a potent inhibitor of HER3/AKT phosphorylation and proliferation in HER2-amplified and NRG1-expressing cancer cells, and it displayed single-agent efficacy in tumor xenograft models. Combining LJM716 with agents that target HER2 or EGFR produced synergistic antitumor activity in vitro and in vivo. In particular, combining LJM716 with trastuzumab produced a more potent inhibition of signaling and cell proliferation than trastuzumab/pertuzumab combinations with similar activity in vivo. To elucidate its mechanism of action, we solved the structure of LJM716 bound to HER3, finding that LJM716 bound to an epitope, within domains 2 and 4, that traps HER3 in an inactive conformation. Taken together, our findings establish that LJM716 possesses a novel mechanism of action that, in combination with HER2- or EGFR-targeted agents, may leverage their clinical efficacy in ErbB-driven cancers.


  • Organizational Affiliation

    Authors' Affiliations: Novartis Institutes for Biomedical Research, Cambridge, Massachusetts; Departments of Medicine and Cancer Biology; Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee; MorphoSys AG, Martinsried, Germany; and Genomics Institute of the Novartis Research Foundation, San Diego, California.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor tyrosine-protein kinase erbB-3627Homo sapiensMutation(s): 0 
Gene Names: ERBB3HER3
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P21860 (Homo sapiens)
Explore P21860 
Go to UniProtKB:  P21860
PHAROS:  P21860
GTEx:  ENSG00000065361 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21860
Glycosylation
Glycosylation Sites: 5Go to GlyGen: P21860-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MOR09825 Fab fragment heavy chainB [auth H]238Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MOR09825 Fab fragment light chainC [auth L]214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth B],
E [auth C]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.226α = 90
b = 140.939β = 90
c = 180.247γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references
  • Version 1.2: 2014-12-17
    Changes: Database references
  • Version 1.3: 2015-02-25
    Changes: Derived calculations
  • Version 1.4: 2015-03-18
    Changes: Non-polymer description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Source and taxonomy, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary