4GL9

Crystal structure of inhibitory protein SOCS3 in complex with JAK2 kinase domain and fragment of GP130 intracellular domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

SOCS3 binds specific receptor-JAK complexes to control cytokine signaling by direct kinase inhibition.

Kershaw, N.J.Murphy, J.M.Liau, N.P.Varghese, L.N.Laktyushin, A.Whitlock, E.L.Lucet, I.S.Nicola, N.A.Babon, J.J.

(2013) Nat.Struct.Mol.Biol. 20: 469-476

  • DOI: 10.1038/nsmb.2519

  • PubMed Abstract: 
  • The inhibitory protein SOCS3 plays a key part in the immune and hematopoietic systems by regulating signaling induced by specific cytokines. SOCS3 functions by inhibiting the catalytic activity of Janus kinases (JAKs) that initiate signaling within t ...

    The inhibitory protein SOCS3 plays a key part in the immune and hematopoietic systems by regulating signaling induced by specific cytokines. SOCS3 functions by inhibiting the catalytic activity of Janus kinases (JAKs) that initiate signaling within the cell. We determined the crystal structure of a ternary complex between mouse SOCS3, JAK2 (kinase domain) and a fragment of the interleukin-6 receptor β-chain. The structure shows that SOCS3 binds JAK2 and receptor simultaneously, using two opposing surfaces. While the phosphotyrosine-binding groove on the SOCS3 SH2 domain is occupied by receptor, JAK2 binds in a phosphoindependent manner to a noncanonical surface. The kinase-inhibitory region of SOCS3 occludes the substrate-binding groove on JAK2, and biochemical studies show that it blocks substrate association. These studies reveal that SOCS3 targets specific JAK-cytokine receptor pairs and explains the mechanism and specificity of SOCS action.


    Organizational Affiliation

    Department of Structural Biology, Walter and Eliza Hall Institute, Parkville, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase
A, B, C, D
297Mus musculusMutation(s): 0 
Gene Names: Jak2
EC: 2.7.10.2
Find proteins for Q62120 (Mus musculus)
Go to UniProtKB:  Q62120
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Interleukin-6 receptor subunit beta
I, K, J, L
15Mus musculusMutation(s): 0 
Gene Names: Il6st
Find proteins for Q00560 (Mus musculus)
Go to UniProtKB:  Q00560
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Suppressor of cytokine signaling 3,Suppressor of cytokine signaling 3,Suppressor of cytokine signaling 3,Suppressor of cytokine signaling 3
E, F, G, H
143Mus musculusMutation(s): 0 
Gene Names: Socs3 (Cis3, Cish3)
Find proteins for O35718 (Mus musculus)
Go to UniProtKB:  O35718
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
IZA
Query on IZA

Download SDF File 
Download CCD File 
A, B, C, D
2-TERT-BUTYL-9-FLUORO-3,6-DIHYDRO-7H-BENZ[H]-IMIDAZ[4,5-F]ISOQUINOLINE-7-ONE
2-(1,1-DIMETHYLETHYL)9-FLUORO-3,6-DIHYDRO-7H-BENZ[H]-IMIDAZ[4,5-F]ISOQUINOLIN-7-ONE
C18 H16 F N3 O
VNDWQCSOSCCWIP-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A, B, C, D, I, J, K, L
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IZAIC50: 1 - 1400 nM (96) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.249 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 139.262α = 90.00
b = 139.262β = 90.00
c = 316.742γ = 120.00
Software Package:
Software NamePurpose
Blu-Icedata collection
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-04-17
    Type: Database references
  • Version 1.2: 2015-03-04
    Type: Structure summary
  • Version 1.3: 2017-08-09
    Type: Data collection, Refinement description, Source and taxonomy
  • Version 1.4: 2018-06-13
    Type: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary