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 1.3 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: https://doi.org/10.1016/j.molcel.2004.12.031
  • Primary Citation of Related Structures:  
    1U5S

  • 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, 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytoplasmic protein NCK271Homo sapiensMutation(s): 0 
Gene Names: NCK2
UniProt & NIH Common Fund Data Resources
Find proteins for O43639 (Homo sapiens)
Explore O43639 
Go to UniProtKB:  O43639
PHAROS:  O43639
GTEx:  ENSG00000071051 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43639
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PINCH protein66Homo sapiensMutation(s): 0 
Gene Names: LIMS1
UniProt & NIH Common Fund Data Resources
Find proteins for P48059 (Homo sapiens)
Explore P48059 
Go to UniProtKB:  P48059
PHAROS:  P48059
GTEx:  ENSG00000169756 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48059
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth B],
D [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
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 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Database references, Derived calculations