6C7Y | pdb_00006c7y

Crystal structure of inhibitory protein SOCS1 in complex with JAK1 kinase domain

• PDB DOI: https://doi.org/10.2210/pdb6C7Y/pdb

• Classification: SIGNALING PROTEIN, TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens, Gallus gallus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2018-01-23 Released: 2018-05-02 
• Deposition Author(s): Liau, N.P.D., Laktyushin, A., Lucet, I.S., Murphy, J.M., Yao, S., Callaghan, K., Nicola, N.A., Kershaw, N.J., Babon, J.J.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.241 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Models: experimental

Literature

The molecular basis of JAK/STAT inhibition by SOCS1.

Liau, N.P.D., Laktyushin, A., Lucet, I.S., Murphy, J.M., Yao, S., Whitlock, E., Callaghan, K., Nicola, N.A., Kershaw, N.J., Babon, J.J.

(2018) Nat Commun 9: 1558-1558

• PubMed: 29674694 
• DOI: https://doi.org/10.1038/s41467-018-04013-1
• Primary Citation Related Structures: 
  6C5X, 6C7Y


• PubMed Abstract: 
  

  The SOCS family of proteins are negative-feedback inhibitors of signalling induced by cytokines that act via the JAK/STAT pathway. SOCS proteins can act as ubiquitin ligases by recruiting Cullin5 to ubiquitinate signalling components; however, SOCS1, the most potent member of the family, can also inhibit JAK directly. Here we determine the structural basis of both these modes of inhibition. Due to alterations within the SOCS box domain, SOCS1 has a compromised ability to recruit Cullin5; however, it is a direct, potent and selective inhibitor of JAK catalytic activity. The kinase inhibitory region of SOCS1 targets the substrate binding groove of JAK with high specificity and thereby blocks any subsequent phosphorylation. SOCS1 is a potent inhibitor of the interferon gamma (IFNγ) pathway, however, it does not bind the IFNγ receptor, making its mode-of-action distinct from SOCS3. These findings reveal the mechanism used by SOCS1 to inhibit signalling by inflammatory cytokines.

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Organizational Affiliation: 
• Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, VIC, 3052, Australia.
The University of Melbourne, Royal Parade, Parkville, VIC, 3050, Australia.
Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, VIC, 3052, Australia. [e-mail].
The University of Melbourne, Royal Parade, Parkville, VIC, 3050, Australia. [e-mail].
Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, VIC, 3052, Australia. [e-mail].
The University of Melbourne, Royal Parade, Parkville, VIC, 3050, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 46.82 kDa 
• Atom Count: 3,135 
• Modeled Residue Count: 391 
• Deposited Residue Count: 403 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK1	A	286	Homo sapiens	Mutation(s): 0  Gene Names: JAK1, JAK1A, JAK1B EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P23458 (Homo sapiens) Explore P23458  Go to UniProtKB:  P23458
PHAROS:  P23458 GTEx:  ENSG00000162434

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Suppressor of cytokine signaling 1	B	117	Gallus gallus	Mutation(s): 0  Gene Names: SOCS1
UniProt
Find proteins for B6RCQ2 (Gallus gallus) Explore B6RCQ2  Go to UniProtKB:  B6RCQ2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
EDO	F [auth A], G [auth A], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	I [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.241 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.926	α = 90
b = 83.926	β = 90
c = 161.438	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-05-02 
Deposition Author(s): Liau, N.P.D., Laktyushin, A., Lucet, I.S., Murphy, J.M., Yao, S., Callaghan, K., Nicola, N.A., Kershaw, N.J., Babon, J.J.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	112299
National Health and Medical Research Council (NHMRC, Australia)	Australia	1113577
National Health and Medical Research Council (NHMRC, Australia)	Australia	361646

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-11-13
  Changes: Structure summary