5CUS

Crystal Structure of sErbB3-Fab3379 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Inhibition of ErbB3 by a monoclonal antibody that locks the extracellular domain in an inactive configuration.

Lee, S.Greenlee, E.B.Amick, J.R.Ligon, G.F.Lillquist, J.S.Natoli, E.J.Hadari, Y.Alvarado, D.Schlessinger, J.

(2015) Proc.Natl.Acad.Sci.USA 112: 13225-13230

  • DOI: 10.1073/pnas.1518361112

  • PubMed Abstract: 
  • ErbB3 (HER3) is a member of the EGF receptor (EGFR) family of receptor tyrosine kinases, which, unlike the other three family members, contains a pseudo kinase in place of a tyrosine kinase domain. In cancer, ErbB3 activation is driven by a ligand-de ...

    ErbB3 (HER3) is a member of the EGF receptor (EGFR) family of receptor tyrosine kinases, which, unlike the other three family members, contains a pseudo kinase in place of a tyrosine kinase domain. In cancer, ErbB3 activation is driven by a ligand-dependent mechanism through the formation of heterodimers with EGFR, ErbB2, or ErbB4 or via a ligand-independent process through heterodimerization with ErbB2 overexpressed in breast tumors or other cancers. Here we describe the crystal structure of the Fab fragment of an antagonistic monoclonal antibody KTN3379, currently in clinical development in human cancer patients, in complex with the ErbB3 extracellular domain. The structure reveals a unique allosteric mechanism for inhibition of ligand-dependent or ligand-independent ErbB3-driven cancers by binding to an epitope that locks ErbB3 in an inactive conformation. Given the similarities in the mechanism of ErbB receptor family activation, these findings could facilitate structure-based design of antibodies that inhibit EGFR and ErbB4 by an allosteric mechanism.


    Organizational Affiliation

    Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor tyrosine-protein kinase erbB-3
A, B, C, D
627Homo sapiensMutation(s): 0 
Gene Names: ERBB3 (HER3)
EC: 2.7.10.1
Find proteins for P21860 (Homo sapiens)
Go to Gene View: ERBB3
Go to UniProtKB:  P21860
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IgG H chain
H, I, J, K
221N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab LC region of KTN3379
L, M, N, O
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, M
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.252 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 84.378α = 87.10
b = 127.141β = 85.54
c = 138.078γ = 89.92
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-10-28
    Type: Database references
  • Version 1.2: 2015-11-04
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Advisory, Database references, Derived calculations, Refinement description