3D8F

Crystal structure of the human Fe65-PTB1 domain with bound phosphate (trigonal crystal form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the human Fe65-PTB1 domain.

Radzimanowski, J.Ravaud, S.Schlesinger, S.Koch, J.Beyreuther, K.Sinning, I.Wild, K.

(2008) J Biol Chem 283: 23113-23120

  • DOI: 10.1074/jbc.M800861200
  • Primary Citation of Related Structures:  
    3D8D, 3D8E, 3D8F

  • PubMed Abstract: 
  • The neuronal adaptor protein Fe65 is involved in brain development, Alzheimer disease amyloid precursor protein (APP) signaling, and proteolytic processing of APP. It contains three protein-protein interaction domains, one WW domain, and a unique tandem array of phosphotyrosine-binding (PTB) domains ...

    The neuronal adaptor protein Fe65 is involved in brain development, Alzheimer disease amyloid precursor protein (APP) signaling, and proteolytic processing of APP. It contains three protein-protein interaction domains, one WW domain, and a unique tandem array of phosphotyrosine-binding (PTB) domains. The N-terminal PTB domain (Fe65-PTB1) was shown to interact with a variety of proteins, including the low density lipoprotein receptor-related protein (LRP-1), the ApoEr2 receptor, and the histone acetyltransferase Tip60. We have determined the crystal structures of human Fe65-PTB1 in its apo- and in a phosphate-bound form at 2.2 and 2.7A resolution, respectively. The overall fold shows a PTB-typical pleckstrin homology domain superfold. Although Fe65-PTB1 has been classified on an evolutionary basis as a Dab-like PTB domain, it contains attributes of other PTB domain subfamilies. The phosphotyrosine-binding pocket resembles IRS-like PTB domains, and the bound phosphate occupies the binding site of the phosphotyrosine (Tyr(P)) within the canonical NPXpY recognition motif. In addition Fe65-PTB1 contains a loop insertion between helix alpha2 and strand beta2(alpha2/beta2 loop) similar to members of the Shc-like PTB domain subfamily. The structural comparison with the Dab1-PTB domain reveals a putative phospholipid-binding site opposite the peptide binding pocket. We suggest Fe65-PTB1 to interact with its target proteins involved in translocation and signaling of APP in a phosphorylation-dependent manner.


    Related Citations: 
    • Mercury-induced crystallization and SAD phasing of the human Fe65-PTB1 domain.
      Radzimanowski, J., Ravaud, S., Beyreuther, K., Sinning, I., Wild, K.
      (2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 382

    Organizational Affiliation

    Heidelberg University Biochemistry Center, INF328, D-69120 Heidelberg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Amyloid beta A4 precursor protein-binding family B member 1A, B, C, D148Homo sapiensMutation(s): 0 
Gene Names: APBB1FE65RIR
Find proteins for O00213 (Homo sapiens)
Explore O00213 
Go to UniProtKB:  O00213
NIH Common Fund Data Resources
PHAROS:  O00213
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A], F [auth C]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.04α = 90
b = 146.04β = 90
c = 78.294γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance