Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 22987.98 
• Atom Count: 1580 
• Residue Count: 200 
• Unique protein chains: 2

2BBA

Crystal Structure and Thermodynamic Characterization of the EphB4 Receptor in Complex with an ephrin-B2 Antagonist Peptide Reveals the Determinants for Receptor Specificity.

• DOI: 10.2210/pdb2BBA/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 2005-10-17 Released: 2006-07-18 
• Deposition Author(s): Chrencik, J.E., Kuhn, P., Accelerated Technologies Center for Gene to 3D Structure (ATCG3D)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.191 
• R-Value Work: 0.174 

Literature

Structure and thermodynamic characterization of the EphB4/Ephrin-B2 antagonist peptide complex reveals the determinants for receptor specificity.

Chrencik, J.E., Brooun, A., Recht, M.I., Kraus, M.L., Koolpe, M., Kolatkar, A.R., Bruce, R.H., Martiny-Baron, G., Widmer, H., Pasquale, E.B., Kuhn, P.

(2006) Structure 14: 321-330

• PubMed: 16472751 
• DOI: 10.1016/j.str.2005.11.011


• PubMed Abstract: 
  

The Eph receptor tyrosine kinases and their ligands, the ephrins, regulate numerous biological processes in developing and adult tissues and have been implicated in cancer progression and in pathological forms of angiogenesis. We report the crystal structure of the EphB4 receptor in complex with a highly specific antagonistic peptide at a resolution of 1.65 angstroms. The peptide is situated in a hydrophobic cleft of EphB4 corresponding to the cleft in EphB2 occupied by the ephrin-B2 G-H loop, consistent with its antagonistic properties. Structural analysis identifies several residues within the EphB4 binding cleft that likely determine the ligand specificity of this receptor, while isothermal titration calorimetry experiments with truncated forms of the peptide define the amino acid residues of the peptide that are critical for receptor binding. These studies reveal structural features that will aid drug discovery initiatives to develop EphB4 antagonists for therapeutic applications.

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Organizational Affiliation: 

Department of Cellular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ephrin type-B receptor 4	A	185	Homo sapiens	Mutation(s): 0  Gene Names: EPHB4 (HTK, MYK1, TYRO11) EC: 2.7.10.1
Find proteins for P54760 (Homo sapiens) Go to Gene View: EPHB4 Go to UniProtKB:  P54760

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Agonist peptide	P	15	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.191 
• R-Value Work: 0.174 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 60.972	α = 90.00
b = 60.972	β = 90.00
c = 151.681	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-17 
• Released Date: 2006-07-18 
• Deposition Author(s): Chrencik, J.E., Kuhn, P., Accelerated Technologies Center for Gene to 3D Structure (ATCG3D)

Revision History 

• Version 1.0: 2006-07-18
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Version format compliance