7OM4

Nanobody EgB4 bound to the full extracellular EGFR-EGF complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.05 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.296 
  • R-Value Observed: 0.297 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the non-inhibitory mechanism of the anti-EGFR EgB4 nanobody.

Zeronian, M.R.Doulkeridou, S.van Bergen En Henegouwen, P.M.P.Janssen, B.J.C.

(2022) BMC Mol Cell Biol 23: 12-12

  • DOI: https://doi.org/10.1186/s12860-022-00412-x
  • Primary Citation of Related Structures:  
    7OM4, 7OM5

  • PubMed Abstract: 

    The epidermal growth factor receptor (EGFR) is involved in various developmental processes, and alterations of its extracellular segment are associated with several types of cancers, in particular glioblastoma multiforme (GBM). The EGFR extracellular region is therefore a primary target for therapeutic agents, such as monoclonal antibodies and variable domains of heavy chain antibodies (VHH), also called nanobodies. Nanobodies have been previously shown to bind to EGFR, and to inhibit ligand-mediated EGFR activation. Here we present the X-ray crystal structures of the EgB4 nanobody, alone (to 1.48 Å resolution) and bound to the full extracellular EGFR-EGF complex in its active conformation (to 6.0 Å resolution). We show that EgB4 binds to a new epitope located on EGFR domains I and II, and we describe the molecular mechanism by which EgB4 plays a non-inhibitory role in EGFR signaling. This work provides the structural basis for the application of EgB4 as a tool for research, for targeted therapy, or as a biomarker to locate EGFR-associated tumors, all without affecting EGFR activation.


  • Organizational Affiliation

    Structural Biochemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor630Homo sapiensMutation(s): 0 
Gene Names: EGFRERBBERBB1HER1
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
PHAROS:  P00533
GTEx:  ENSG00000146648 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00533
Glycosylation
Glycosylation Sites: 7Go to GlyGen: P00533-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factorB [auth C]53Homo sapiensMutation(s): 0 
Gene Names: EGF
UniProt & NIH Common Fund Data Resources
Find proteins for P01133 (Homo sapiens)
Explore P01133 
Go to UniProtKB:  P01133
PHAROS:  P01133
GTEx:  ENSG00000138798 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01133
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody EgB4C [auth B]130Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.05 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.296 
  • R-Value Observed: 0.297 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 307.61α = 90
b = 307.61β = 90
c = 135.138γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
PHASERphasing
STARANISOdata scaling
XDSdata reduction
autoPROCdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-03-23
    Changes: Database references, Refinement description
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description