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PDBsum entry 3czu

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protein ligands Protein-protein interface(s) links
Transferase/signaling protein PDB id
3czu
Jmol
Contents
Protein chains
175 a.a. *
130 a.a. *
Ligands
NAG-NAG-MAN
Waters ×73
* Residue conservation analysis
PDB id:
3czu
Name: Transferase/signaling protein
Title: Crystal structure of the human ephrin a2- ephrin a1 complex
Structure: Ephrin type-a receptor 2. Chain: a. Fragment: ligand binding domain: residues 23-202. Synonym: tyrosine-protein kinase receptor eck, epithelial c kinase. Engineered: yes. Ephrin-a1. Chain: b. Fragment: residues 17-171.
Source: Homo sapiens. Organism_taxid: 9606. Gene: epha2, eck. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Gene: efna1, eplg1, lerk1, tnfaip4.
Resolution:
2.65Å     R-factor:   0.195     R-free:   0.225
Authors: J.R.Walker,L.Yermekbayeva,A.Seitova,C.Butler-Cole,C.Bountra, M.Wikstrom,C.H.Arrowsmith,A.M.Edwards,A.Bochkarev,S.Dhe-Pag Structural Genomics Consortium (Sgc)
Key ref: J.P.Himanen et al. (2010). Architecture of Eph receptor clusters. Proc Natl Acad Sci U S A, 107, 10860-10865. PubMed id: 20505120
Date:
30-Apr-08     Release date:   12-Aug-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P29317  (EPHA2_HUMAN) -  Ephrin type-A receptor 2
Seq:
Struc:
 
Seq:
Struc:
976 a.a.
175 a.a.
Protein chain
Pfam   ArchSchema ?
B2R7U1  (B2R7U1_HUMAN) -  cDNA, FLJ93602, highly similar to Homo sapiens ephrin-A1 (EFNA1), mRNA
Seq:
Struc:
205 a.a.
130 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chain A: E.C.2.7.10.1  - Receptor protein-tyrosine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
ATP
+
[protein]-L-tyrosine
Bound ligand (Het Group name = NAG)
matches with 47.62% similarity
= ADP
+ [protein]-L-tyrosine phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     transmembrane receptor protein tyrosine kinase signaling pathway   3 terms 
  Biochemical function     ATP binding     2 terms  

 

 
    reference    
 
 
Proc Natl Acad Sci U S A 107:10860-10865 (2010)
PubMed id: 20505120  
 
 
Architecture of Eph receptor clusters.
J.P.Himanen, L.Yermekbayeva, P.W.Janes, J.R.Walker, K.Xu, L.Atapattu, K.R.Rajashankar, A.Mensinga, M.Lackmann, D.B.Nikolov, S.Dhe-Paganon.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21269602 J.Brasch, O.J.Harrison, G.Ahlsen, S.M.Carnally, R.M.Henderson, B.Honig, and L.Shapiro (2011).
Structure and binding mechanism of vascular endothelial cadherin: a divergent classical cadherin.
  J Mol Biol, 408, 57-73.
PDB code: 3ppe
21439481 N.Singla, H.Erdjument-Bromage, J.P.Himanen, T.W.Muir, and D.B.Nikolov (2011).
A semisynthetic Eph receptor tyrosine kinase provides insight into ligand-induced kinase activation.
  Chem Biol, 18, 361-371.  
20717138 I.Bethani, S.S.Skånland, I.Dikic, and A.Acker-Palmer (2010).
Spatial organization of transmembrane receptor signalling.
  EMBO J, 29, 2677-2688.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.