PDBsum entry 1u5s

Metal binding protein

PDB id: 1u5s

Contents

Protein chains

71 a.a. *

66 a.a. *

Metals

_ZN ×2

* Residue conservation analysis

PDB id:

1u5s

Name:

Metal binding protein

Title:

Nmr structure of the complex between nck-2 sh3 domain and pinch-1 lim4 domain

Structure:

Cytoplasmic protein nck2. Chain: a. Fragment: third sh3 domain (residues 192-262). Synonym: nck adaptor protein 2, sh2/sh3 adaptor protein nck-beta, nck-2. Engineered: yes. Pinch protein. Chain: b. Fragment: fourth lim domain (residues 188-251).

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: nck2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: lims1.

NMR struc:

18 models

Authors:

J.Vaynberg,T.Fukuda,O.Vinogradova,A.Velyvis,L.Ng,C.Wu,J.Qin

Key ref:

J.Vaynberg et al. (2005). Structure of an ultraweak protein-protein complex and its crucial role in regulation of cell morphology and motility. Mol Cell, 17, 513-523. PubMed id: 15721255 DOI: 10.1016/j.molcel.2004.12.031

Date:

28-Jul-04 Release date: 05-Apr-05

Protein chain

O43639  (NCK2_HUMAN) -  Cytoplasmic protein NCK2 from Homo sapiens

Seq: 380 a.a.

Struc: 71 a.a.

Protein chain

P48059  (LIMS1_HUMAN) -  LIM and senescent cell antigen-like-containing domain protein 1 from Homo sapiens

Seq: 325 a.a.

Struc: 66 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.?

DOI no: 10.1016/j.molcel.2004.12.031

Mol Cell 17:513-523 (2005)

PubMed id: 15721255

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

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

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.

Selected figure(s)

Figure 2.
Figure 2. Distinct Binding Modes of SH3-3 and LIM4 Domains(A) Sequence alignment for SH3-3 and LIM4 with other representative homologs. For representative SH3 domains, CSK (Ghose et al., 2001), p67^phox (Kami et al., 2002), and ScPex13P (Pires et al., 2003) were chosen based on the fact that their crystal structures are available for comparison and that the former two recognize conventional PXXP motifs and the last recognizes a nonconventional sequence. Note that the recognition sequences for Csk and p67phox are not in Table 2 (only non-PxxP binding sequences are in Table 2). Also, although residues marked in blue are essential for PXXP binding, other neighboring residues in the sequence could be potentially involved in binding to immediate regions of the N or C terminus of the PXXP ligand. For the LIM domain, PINCH LIM1 and LMO4 were chosen because their binding modes have been published (Velyvis et al. 2001; Velyvis et al. 2003 and Deane et al. 2003). The binding interface residues for Nck-2 SH3-3 are marked in red and are contrasted to conventional PxxP binding sites in CSK_Hum and p67^phox_Hum (blue), nonconventional binding sites in CSK_Hum and p67^phox_Hum (orange), and ScPex13P (magenta). The binding interface residues for PINCH-1 LIM4 are marked in red and are contrasted to those in PINCH-1 LIM1 and LMO4 (green).(B) The conventional and nonconventional binding site residues for SH3 domains in (A) are projected to the SH3-3 surface. PPII: conventional PxxP ligand binding site. Both CSK and p67phox SH3 domains have conventional and nonconventional binding sites. ScPex13P SH3 has an entirely nonconventional binding mode (magenta), which is better seen by rotating the surface 90° counterclockwise around the z axis. However, all of these binding sites are different from the Nck-2 SH3-3 binding site by LIM4.(C) The binding site residues for the LIM domains in (A) are projected to the PINCH-1 LIM4 surface, showing that the LIM4 binding site for SH3-3 is distinct from those of LMO4 and PINCH-1 LIM1.

Figure 6.
Figure 6. Diagram of a Complex Network Involved in the Cell-Matrix Adhesion Regulation of Actin CytoskeletonThe complex network that involves PINCH-1 and Nck-2 provides insight into how the ultraweak Nck-2/PINCH-1 interaction transiently contributes to the stability and dynamics of the supermolecular complex. The transient association of Nck-2/PINCH-1 may facilitate the rapid assembly/disassembly of the complex during cell shape modulation and movement. All proteins labeled in the diagram have been shown to be involved in the network (see reviews by Wu 1999; Wu and Dedhar 2001; Buday et al. 2002 and Brakebusch and Fassler 2003). The list of proteins in the network is expected to continue to grow.

The above figures are reprinted by permission from Cell Press: Mol Cell (2005, 17, 513-523) copyright 2005.

Figures were selected by an automated process.