2CIA

human nck2 sh2-domain in complex with a decaphosphopeptide from translocated intimin receptor (tir) of epec


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Phosphotyrosine Peptide Binding Specificity of Nck1 and Nck2 Src Homology 2 Domains.

Frese, S.Schubert, W.-D.Findeis, A.C.Marquardt, T.Roske, Y.S.Stradal, T.E.B.Heinz, D.W.

(2006) J.Biol.Chem. 281: 18236

  • DOI: 10.1074/jbc.M512917200
  • Primary Citation of Related Structures:  2CI8, 2CI9

  • PubMed Abstract: 
  • Nck proteins are essential Src homology (SH) 2 and SH3 domain-bearing adapters that modulate actin cytoskeleton dynamics by linking proline-rich effector molecules to tyrosine kinases or phosphorylated signaling intermediates. Two mammalian pathogens ...

    Nck proteins are essential Src homology (SH) 2 and SH3 domain-bearing adapters that modulate actin cytoskeleton dynamics by linking proline-rich effector molecules to tyrosine kinases or phosphorylated signaling intermediates. Two mammalian pathogens, enteropathogenic Escherichia coli and vaccinia virus, exploit Nck as part of their infection strategy. Conflicting data indicate potential differences in the recognition specificities of the SH2 domains of the isoproteins Nck1 (Nckalpha) and Nck2 (Nckbeta and Grb4). We have characterized the binding specificities of both SH2 domains and find them to be essentially indistinguishable. Crystal structures of both domains in complex with phosphopeptides derived from the enteropathogenic E. coli protein Tir concur in identifying highly conserved, specific recognition of the phosphopeptide. Differential peptide recognition can therefore not account for the preference of either Nck in particular signaling pathways. Binding studies using sequentially mutated, high affinity phosphopeptides establish the sequence variability tolerated in peptide recognition. Based on this binding motif, we identify potential new binding partners of Nck1 and Nck2 and confirm this experimentally for the Arf-GAP GIT1.


    Organizational Affiliation

    Division of Cell Biology, German Research Center for Biotechnology, Mascheroder Weg 1, D-38124 Braunschweig, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOPLASMIC PROTEIN NCK2
A
102Homo sapiensGene Names: NCK2 (GRB4)
Find proteins for O43639 (Homo sapiens)
Go to Gene View: NCK2
Go to UniProtKB:  O43639
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TRANSLOCATED INTIMIN RECEPTOR
L
11Escherichia coli O127:H6 (strain E2348/69 / EPEC)Gene Names: tir (espE)
Find proteins for B7UM99 (Escherichia coli O127:H6 (strain E2348/69 / EPEC))
Go to UniProtKB:  B7UM99
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPA
Query on IPA

Download SDF File 
Download CCD File 
A
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
L
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
ACE
Query on ACE
L
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 31.244α = 90.00
b = 52.188β = 90.00
c = 58.100γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
EPMRphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance