3CZU

Crystal structure of the human ephrin A2- ephrin A1 complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Architecture of Eph receptor clusters.

Himanen, J.P., Yermekbayeva, L., Janes, P.W., Walker, J.R., Xu, K., Atapattu, L., Rajashankar, K.R., Mensinga, A., Lackmann, M., Nikolov, D.B., Dhe-Paganon, S.

(2010) Proc.Natl.Acad.Sci.USA 107: 10860-10865

  • DOI: 10.1073/pnas.1004148107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Eph receptor tyrosine kinases and their ephrin ligands regulate cell navigation during normal and oncogenic development. Signaling of Ephs is initiated in a multistep process leading to the assembly of higher-order signaling clusters that set off bid ...

    Eph receptor tyrosine kinases and their ephrin ligands regulate cell navigation during normal and oncogenic development. Signaling of Ephs is initiated in a multistep process leading to the assembly of higher-order signaling clusters that set off bidirectional signaling in interacting cells. However, the structural and mechanistic details of this assembly remained undefined. Here we present high-resolution structures of the complete EphA2 ectodomain and complexes with ephrin-A1 and A5 as the base unit of an Eph cluster. The structures reveal an elongated architecture with novel Eph/Eph interactions, both within and outside of the Eph ligand-binding domain, that suggest the molecular mechanism underlying Eph/ephrin clustering. Structure-function analysis, by using site-directed mutagenesis and cell-based signaling assays, confirms the importance of the identified oligomerization interfaces for Eph clustering.

    Organizational Affiliation: 

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ephrin type-A receptor 2
A
207Homo sapiensMutation(s): 0 
Gene Names: EPHA2 (ECK)
EC: 2.7.10.1
Find proteins for P29317 (Homo sapiens)
Go to Gene View: EPHA2
Go to UniProtKB:  P29317
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ephrin-A1
B
182Homo sapiensMutation(s): 0 
Gene Names: EFNA1 (EPLG1, LERK1, TNFAIP4)
Find proteins for P20827 (Homo sapiens)
Go to Gene View: EFNA1
Go to UniProtKB:  P20827
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN
Download SDF File 
Download CCD File 
B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 99.431α = 90.00
b = 99.431β = 90.00
c = 204.879γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance