3C9A

High Resolution Crystal Structure of Argos bound to the EGF domain of Spitz

• PDB DOI:  https://doi.org/10.2210/pdb3C9A/pdb

• Classification: HORMONE/SIGNALING PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Spodoptera frugiperda, Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2008-02-15 Released: 2008-05-20 
• Deposition Author(s): Klein, D.E., Stayrook, S.E., Shi, F., Narayan, K., Lemmon, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.240 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 

Literature

Structural basis for EGFR ligand sequestration by Argos.

Klein, D.E., Stayrook, S.E., Shi, F., Narayan, K., Lemmon, M.A.

(2008) Nature 453: 1271-1275

• PubMed: 18500331 
• DOI: https://doi.org/10.1038/nature06978
• Primary Citation of Related Structures:  
  3C9A, 3CA7, 3CGU


• PubMed Abstract: 
  

Members of the epidermal growth factor receptor (EGFR) or ErbB/HER family and their activating ligands are essential regulators of diverse developmental processes. Inappropriate activation of these receptors is a key feature of many human cancers, and its reversal is an important clinical goal. A natural secreted antagonist of EGFR signalling, called Argos, was identified in Drosophila. We showed previously that Argos functions by directly binding (and sequestering) growth factor ligands that activate EGFR. Here we describe the 1.6-A resolution crystal structure of Argos bound to an EGFR ligand. Contrary to expectations, Argos contains no EGF-like domain. Instead, a trio of closely related domains (resembling a three-finger toxin fold) form a clamp-like structure around the bound EGF ligand. Although structurally unrelated to the receptor, Argos mimics EGFR by using a bipartite binding surface to entrap EGF. The individual Argos domains share unexpected structural similarities with the extracellular ligand-binding regions of transforming growth factor-beta family receptors. The three-domain clamp of Argos also resembles the urokinase-type plasminogen activator (uPA) receptor, which uses a similar mechanism to engulf the EGF-like module of uPA. Our results indicate that undiscovered mammalian counterparts of Argos may exist among other poorly characterized structural homologues. In addition, the structures presented here define requirements for the design of artificial EGF-sequestering proteins that would be valuable anti-cancer therapeutics.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 809C Stellar-Chance Laboratories, 422 Curie Boulevard, Philadelphia, Pennsylvania 19104-6059, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.7 kDa 
• Atom Count: 4,966 
• Modelled Residue Count: 511 
• Deposited Residue Count: 550 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein giant-lens	A, B	223	Drosophila melanogaster	Mutation(s): 0  Gene Names: argos, aos, gil, sty
UniProt
Find proteins for Q00805 (Drosophila melanogaster) Explore Q00805  Go to UniProtKB:  Q00805

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein spitz	C, D	52	Drosophila melanogaster	Mutation(s): 0  Gene Names: spi, CG10334
UniProt
Find proteins for Q01083 (Drosophila melanogaster) Explore Q01083  Go to UniProtKB:  Q01083

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth C], V [auth D]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.240 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.991	α = 84.23
b = 51.275	β = 74.82
c = 69.985	γ = 75.67

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-20 
Deposition Author(s): Klein, D.E., Stayrook, S.E., Shi, F., Narayan, K., Lemmon, M.A.

Revision History  

• Version 1.0: 2008-05-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-16
  Changes: Source and taxonomy
• Version 1.3: 2017-10-25
  Changes: Refinement description