PDBsum entry: 1mr1

Signaling protein

PDB id: 1mr1

Contents

Protein chains

195 a.a. *

97 a.a. *

Metals

_ZN ×2

Waters ×16

* Residue conservation analysis

PDB id:

1mr1

Name:

Signaling protein

Title:

Crystal structure of a smad4-ski complex

Structure:

Mothers against decapentaplegic homolog 4. Chain: a, b. Fragment: mh2 domain. Synonym: smad4, mothers against dpp homolog 4, deletion target in pancreatic carcinoma 4, hsmad4. Engineered: yes. Ski oncogene. Chain: c, d. Fragment: smad4-binding domain.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.85Å R-factor: 0.231 R-free: 0.280

Authors:

J.-W.Wu,A.R.Krawitz,J.Chai,W.Li,F.Zhang,K.Luo,Y.Shi

Key ref:

J.W.Wu et al. (2002). Structural mechanism of Smad4 recognition by the nuclear oncoprotein Ski: insights on Ski-mediated repression of TGF-beta signaling. Cell, 111, 357-367. PubMed id: 12419246 DOI: 10.1016/S0092-8674(02)01006-1

Date:

17-Sep-02 Release date: 21-Jan-03

Protein chains

Q13485  (SMAD4_HUMAN) -  Mothers against decapentaplegic homolog 4

Seq: 552 a.a.

Struc: 195 a.a.

Protein chains

P12755  (SKI_HUMAN) -  Ski oncogene

Seq: 728 a.a.

Struc: 97 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (2 terms)
• Biological process: regulation of transcription, DNA-dependent (1 term)
• Biochemical function: binding (3 terms)

DOI no: 10.1016/S0092-8674(02)01006-1

Cell 111:357-367 (2002)

PubMed id: 12419246

Structural mechanism of Smad4 recognition by the nuclear oncoprotein Ski: insights on Ski-mediated repression of TGF-beta signaling.

J.W.Wu, A.R.Krawitz, J.Chai, W.Li, F.Zhang, K.Luo, Y.Shi.

ABSTRACT

The Ski family of nuclear oncoproteins represses TGF-beta signaling through interactions with the Smad proteins. The crystal structure of the Smad4 binding domain of human c-Ski in complex with the MH2 domain of Smad4 reveals specific recognition of the Smad4 L3 loop region by a highly conserved interaction loop (I loop) from Ski. The Ski binding surface on Smad4 significantly overlaps with that required for binding of the R-Smads. Indeed, Ski disrupts the formation of a functional complex between the Co- and R-Smads, explaining how it could lead to repression of TGF-beta, activin, and BMP responses. Intriguingly, the structure of the Ski fragment, stabilized by a bound zinc atom, resembles the SAND domain, in which the corresponding I loop is responsible for DNA binding.

Selected figure(s)

Figure 1.
Figure 1. Overall Structure of the Smad4/Ski Complex(A) A stereo view of the representative electron density map. The experimental F[o] − F[c] map, shown at 1.5σ, was calculated using phases generated from the molecular replacement solution of Smad4 before modeling the Smad4-Ski interactions. The final refined model of the Ski fragment is shown in cyan, with a few prominent residues colored red.(B) Schematic representation of the Smad4-Ski complex in stereo. Some secondary structural elements are labeled. The zinc atom, shown in red, is coordinated by Cys247, Cys250, His262, and His264. The hydrophobic residues on the interaction loop (I loop) of Ski are highlighted in yellow. All figures except Figures 3A and 5A were prepared using MOLSCRIPT (Klaulis, 1991). Figures 3A and 5A were prepared using GRASP (Nicholls et al., 1991).

Figure 3.
Figure 3. Recognition of Smad4 by Ski(A) Overall view of the interactions. Smad4 (purple) is shown in its surface representation. Ski is shown as a cyan coil, while some of its interface residues are represented in yellow.(B) A stereo view of the hydrogen bond networks at the interface. Part of the I loop forms a parallel β strand with the β7 strand of Smad4 through five intermolecular hydrogen bonds. Tyr513 of Smad4, required for binding to the phosphorylated C terminus of R-Smad, is flipped out of its normal orientation and hydrogen bonds to Thr273 of Ski. Smad4 and Ski are shown in purple and cyan, respectively. Their side chains are colored green and yellow, respectively. Hydrogen bonds are indicated by white dashed lines. Coloring scheme is the same for all other figures.(C) A stereo view of the van der Waals contacts between Smad4 and Ski.(D) Mutation of interface residues in Ski results in the abrogation of binding to Smad4. Flag-tagged wild-type or mutant Ski was cotransfected into 293T cells together with HA-Smad4. Cell lysate was subjected to immunoprecipitation using an anti-Flag antibody, and the Ski bound Smad4 was detected by immunoblotting using an anti-HA antibody.

The above figures are reprinted by permission from Cell Press: Cell (2002, 111, 357-367) copyright 2002.

Figures were selected by the author.