1XOD | pdb_00001xod

Crystal structure of X. tropicalis Spred1 EVH-1 domain

• PDB DOI: https://doi.org/10.2210/pdb1XOD/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Xenopus tropicalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-10-06 Released: 2005-01-25 
• Deposition Author(s): Harmer, N.J., Sivak, J.M., Amaya, E., Blundell, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.177 (Depositor) 
• R-Value Work: 
  0.154 (Depositor) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Models: experimental

Literature

1.15A Crystal structure of the X. tropicalis Spred1 EVH1 domain suggests a fourth distinct peptide-binding mechanism within the EVH1 family

Harmer, N.J., Sivak, J.M., Amaya, E., Blundell, T.L.

(2005) FEBS Lett 579: 1161-1166

• PubMed: 15710406 
• DOI: https://doi.org/10.1016/j.febslet.2004.11.114
• Primary Citation Related Structures: 
  1XOD


• PubMed Abstract: 
  

  The recently described Spred protein family has been implicated in the modulation of receptor tyrosine kinase signalling. We report the crystal structure of the Enabled/vasodilator-stimulated phosphoprotein homology-1 (EVH1) domain from Xenopus tropicalis Spred1, solved to 1.15 A resolution. This structure confirms that the Spred EVH1 adopts the pleckstrin-homology fold, with a similar secondary structure to Enabled. A translation of one of the peptide-binding groove beta-strands narrows this groove, whilst one end of the groove shows structural flexibility. We propose that Spred1 will bind peptides that are less proline-rich than other EVH1 domains, with conformational changes indicating an induced fit.

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Organizational Affiliation: 
• Department of Biochemistry, 80 Tennis Court Road, Cambridge, CB2 1GA, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.03 kDa 
• Atom Count: 2,134 
• Modeled Residue Count: 224 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spred1	A, B	118	Xenopus tropicalis	Mutation(s): 0  Gene Names: Spred1
UniProt
Find proteins for Q66JG9 (Xenopus tropicalis) Explore Q66JG9  Go to UniProtKB:  Q66JG9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.177 (Depositor) 
• R-Value Work:  0.154 (Depositor) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.811	α = 90
b = 38.193	β = 95.68
c = 79.907	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-25 
Deposition Author(s): Harmer, N.J., Sivak, J.M., Amaya, E., Blundell, T.L.

Revision History  

• Version 1.0: 2005-01-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description