Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 45.70 kDa 
• Atom Count: 2603 
• Modelled Residue Count: 305 
• Deposited Residue Count: 389 
• Unique protein chains: 2

3CZU

Crystal structure of the human ephrin A2- ephrin A1 complex

• PDB DOI: 10.2210/pdb3CZU/pdb

• Classification: TRANSFERASE/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2008-04-30 Released: 2008-08-12 
• Deposition Author(s): Walker, J.R., Yermekbayeva, L., Seitova, A., Butler-Cole, C., Bountra, C., Wikstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.225 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

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 U S A 107: 10860-10865

• PubMed: 20505120 
• DOI: 10.1073/pnas.1004148107
• Primary Citation of Related Structures:  
  3C8X, 3CZU, 3FL7, 3MBW, 3MX0


• 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 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin type-A receptor 2	A	207	Homo sapiens	Mutation(s): 0  Gene Names: EPHA2, ECK EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29317 (Homo sapiens) Explore P29317  Go to UniProtKB:  P29317
PHAROS:  P29317

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin-A1	B	182	Homo sapiens	Mutation(s): 1  Gene Names: EFNA1, EPLG1, LERK1, TNFAIP4
UniProt & NIH Common Fund Data Resources
Find proteins for P20827 (Homo sapiens) Explore P20827  Go to UniProtKB:  P20827
PHAROS:  P20827

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.225 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.431	α = 90
b = 99.431	β = 90
c = 204.879	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-04-30 
• Released Date: 2008-08-12 
Deposition Author(s): Walker, J.R., Yermekbayeva, L., Seitova, A., Butler-Cole, C., Bountra, C., Wikstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary