5ZRX | pdb_00005zrx

Crystal Structure of EphA2/SHIP2 Complex

• PDB DOI: https://doi.org/10.2210/pdb5ZRX/pdb

• Classification: PROTEIN BINDING
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-04-25 Released: 2018-05-30 
• Deposition Author(s): Wang, Y., Shang, Y., Li, J., Chen, W., Li, G., Wan, J., Liu, W., Zhang, M.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.191 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Models: experimental

Literature

Specific Eph receptor-cytoplasmic effector signaling mediated by SAM-SAM domain interactions.

Wang, Y., Shang, Y., Li, J., Chen, W., Li, G., Wan, J., Liu, W., Zhang, M.

(2018) Elife 7

• PubMed: 29749928 
• DOI: https://doi.org/10.7554/eLife.35677
• Primary Citation Related Structures: 
  5ZRX, 5ZRY, 5ZRZ


• PubMed Abstract: 
  

  The Eph receptor tyrosine kinase (RTK) family is the largest subfamily of RTKs playing critical roles in many developmental processes such as tissue patterning, neurogenesis and neuronal circuit formation, angiogenesis, etc. How the 14 Eph proteins, via their highly similar cytoplasmic domains, can transmit diverse and sometimes opposite cellular signals upon engaging ephrins is a major unresolved question. Here, we systematically investigated the bindings of each SAM domain of Eph receptors to the SAM domains from SHIP2 and Odin, and uncover a highly specific SAM-SAM interaction-mediated cytoplasmic Eph-effector binding pattern. Comparative X-ray crystallographic studies of several SAM-SAM heterodimer complexes, together with biochemical and cell biology experiments, not only revealed the exquisite specificity code governing Eph/effector interactions but also allowed us to identify SAMD5 as a new Eph binding partner. Finally, these Eph/effector SAM heterodimer structures can explain many Eph SAM mutations identified in patients suffering from cancers and other diseases.

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Organizational Affiliation: 
• Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.
Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Kowloon, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.24 kDa 
• Atom Count: 2,319 
• Modeled Residue Count: 251 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2,Ephrin type-A receptor 2	A, B	159	Mus musculus	Mutation(s): 0  Gene Names: Inppl1, Ship2, Epha2, Eck, Myk2, Sek2 EC: 3.1.3.86 (PDB Primary Data), 2.7.10.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q03145 (Mus musculus) Explore Q03145  Go to UniProtKB:  Q03145
IMPC:  MGI:95278
Find proteins for Q6P549 (Mus musculus) Explore Q6P549  Go to UniProtKB:  Q6P549
UniProt Groups	Q6P549Q03145

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.191 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.283	α = 90
b = 43.344	β = 95.35
c = 46.377	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-05-30 
Deposition Author(s): Wang, Y., Shang, Y., Li, J., Chen, W., Li, G., Wan, J., Liu, W., Zhang, M.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2016YFA0501903

Revision History  

• Version 1.0: 2018-05-30
  Type: Initial release
  
• Version 1.1: 2021-09-15
  Changes: Author supporting evidence, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Refinement description