Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.33 kDa 
• Atom Count: 1305 
• Residue Count: 140 
• Unique protein chains: 2

2VIF

Crystal structure of SOCS6 SH2 domain in complex with a c-KIT phosphopeptide

• DOI: 10.2210/pdb2VIF/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-11-30 Released: 2007-12-25 
• Deposition Author(s): Bullock, A., Pike, A.C.W., Savitsky, P., Keates, T., Pilka, E.S., von Delft, F., Edwards, A., Weigelt, J., Arrowsmith, C.H., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.198 
• R-Value Work: 0.139 
• R-Value Observed: 0.142 

Literature

Structural Basis for C-Kit Inhibition by the Suppressor of Cytokine Signaling 6 (Socs6) Ubiquitin Ligase.

Zadjali, F., Pike, A.C.W., Vesterlund, M., Sun, J., Wu, C., Li, S.S., Ronnstrand, L., Knapp, S., Bullock, A., Flores-Morales, A.

(2011) J Biol Chem 286: 480

• PubMed: 21030588 
• DOI: 10.1074/jbc.M110.173526
• Primary Citation of Related Structures:  
  2VIF


• PubMed Abstract: 
  

The c-KIT receptor tyrosine kinase mediates the cellular response to stem cell factor (SCF). Whereas c-KIT activity is important for the proliferation of hematopoietic cells, melanocytes and germ cells, uncontrolled c-KIT activity contributes to the growth of diverse human tumors. Suppressor of cytokine signaling 6 (SOCS6) is a member of the SOCS family of E3 ubiquitin ligases that can interact with c-KIT and suppress c-KIT-dependent pathways. Here, we analyzed the molecular mechanisms that determine SOCS6 substrate recognition. Our results show that the SH2 domain of SOCS6 is essential for its interaction with c-KIT pY568. The 1.45-Å crystal structure of SOCS6 SH2 domain bound to the c-KIT substrate peptide (c-KIT residues 564-574) revealed a highly complementary and specific interface giving rise to a high affinity interaction (K(d) = 0.3 μm). Interestingly, the SH2 binding pocket extends to substrate residue position pY+6 and envelopes the c-KIT phosphopeptide with a large BG loop insertion that contributes significantly to substrate interaction. We demonstrate that SOCS6 has ubiquitin ligase activity toward c-KIT and regulates c-KIT protein turnover in cells. Our data support a role of SOCS6 as a feedback inhibitor of SCF-dependent signaling and provides molecular data to account for target specificity within the SOCS family of ubiquitin ligases.

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Organizational Affiliation: 

Department of Molecular Medicine and Surgery, Karolinska Institutet, SE-17177 Stockholm, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUPPRESSOR OF CYTOKINE SIGNALLING 6	A	141	Homo sapiens	Mutation(s): 0  Gene Names: SOCS6, CIS4, SOCS4
Find proteins for O14544 (Homo sapiens) Explore O14544  Go to UniProtKB:  O14544
NIH Common Fund Data Resources
PHAROS:  O14544 GTEx:  ENSG00000170677

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MAST/STEM CELL GROWTH FACTOR RECEPTOR	P	11	Homo sapiens	Mutation(s): 0  Gene Names: KIT, SCFR EC: 2.7.10.1
Find proteins for P10721 (Homo sapiens) Explore P10721  Go to UniProtKB:  P10721
NIH Common Fund Data Resources
PHAROS:  P10721 GTEx:  ENSG00000157404

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	P	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.198 
• R-Value Work: 0.139 
• R-Value Observed: 0.142 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.377	α = 90
b = 60.143	β = 90
c = 71.367	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-11-30 
• Released Date: 2007-12-25 
Deposition Author(s): Bullock, A., Pike, A.C.W., Savitsky, P., Keates, T., Pilka, E.S., von Delft, F., Edwards, A., Weigelt, J., Arrowsmith, C.H., Knapp, S.

Revision History 

• Version 1.0: 2007-12-25
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance