1U5S

NMR structure of the complex between Nck-2 SH3 domain and PINCH-1 LIM4 domain


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 18 
  • Selection Criteria: structures with the most reperesentative side chains orientations on the complex interface 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of an ultraweak protein-protein complex and its crucial role in regulation of cell morphology and motility.

Vaynberg, J.Fukuda, T.Chen, K.Vinogradova, O.Velyvis, A.Tu, Y.Ng, L.Wu, C.Qin, J.

(2005) Mol.Cell 17: 513-523

  • DOI: 10.1016/j.molcel.2004.12.031

  • PubMed Abstract: 
  • Weak protein-protein interactions (PPIs) (K(D) > 10(-6) M) are critical determinants of many biological processes. However, in contrast to a large growing number of well-characterized, strong PPIs, the weak PPIs, especially those with K(D) > 10(-4) M ...

    Weak protein-protein interactions (PPIs) (K(D) > 10(-6) M) are critical determinants of many biological processes. However, in contrast to a large growing number of well-characterized, strong PPIs, the weak PPIs, especially those with K(D) > 10(-4) M, are poorly explored. Genome wide, there exist few 3D structures of weak PPIs with K(D) > 10(-4) M, and none with K(D) > 10(-3) M. Here, we report the NMR structure of an extremely weak focal adhesion complex (K(D) approximately 3 x 10(-3) M) between Nck-2 SH3 domain and PINCH-1 LIM4 domain. The structure exhibits a remarkably small and polar interface with distinct binding modes for both SH3 and LIM domains. Such an interface suggests a transient Nck-2/PINCH-1 association process that may trigger rapid focal adhesion turnover during integrin signaling. Genetic rescue experiments demonstrate that this interface is indeed involved in mediating cell shape change and migration. Together, the data provide a molecular basis for an ultraweak PPI in regulating focal adhesion dynamics during integrin signaling.


    Organizational Affiliation

    Structural Biology Program, Lerner Research Institute, The Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytoplasmic protein NCK2
A
71Homo sapiensGene Names: NCK2 (GRB4)
Find proteins for O43639 (Homo sapiens)
Go to Gene View: NCK2
Go to UniProtKB:  O43639
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PINCH protein
B
66Homo sapiensGene Names: LIMS1 (PINCH, PINCH1)
Find proteins for P48059 (Homo sapiens)
Go to Gene View: LIMS1
Go to UniProtKB:  P48059
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 18 
  • Selection Criteria: structures with the most reperesentative side chains orientations on the complex interface 
  • Olderado: 1U5S Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance