7OM4

Nanobody EgB4 bound to the full extracellular EGFR-EGF complex

• PDB DOI: https://doi.org/10.2210/pdb7OM4/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Lama glama
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2021-05-21 Released: 2022-03-02 
• Deposition Author(s): Zeronian, M.R., Janssen, B.J.C.

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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 

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

• PubMed: 35232398 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 91.68 kDa 
• Atom Count: 6,204 
• Modelled Residue Count: 791 
• Deposited Residue Count: 813 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	630	Homo sapiens	Mutation(s): 0  Gene Names: EGFR, ERBB, ERBB1, HER1 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor	B [auth C]	53	Homo sapiens	Mutation(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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody EgB4	C [auth B]	130	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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 = 307.61	α = 90
b = 307.61	β = 90
c = 135.138	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
PHASER	phasing
STARANISO	data scaling
XDS	data reduction
autoPROC	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Zeronian, M.R., Janssen, B.J.C.

Revision History  

• 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