6I4X

Crystal structure of SOCS2:Elongin C:Elongin B in complex with erythropoietin receptor peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase.

Kung, W.W., Ramachandran, S., Makukhin, N., Bruno, E., Ciulli, A.

(2019) Nat Commun 10: 2534-2534

  • DOI: 10.1038/s41467-019-10190-4
  • Primary Citation of Related Structures:  
    6I4X, 6I5J, 6I5N

  • PubMed Abstract: 

    • The suppressor of cytokine signaling 2 (SOCS2) acts as substrate recognition subunit of a Cullin5 E3 ubiquitin ligase complex. SOCS2 binds to phosphotyrosine-modified epitopes as degrons for ubiquitination and proteasomal degradation, yet the molecular b ...

    The suppressor of cytokine signaling 2 (SOCS2) acts as substrate recognition subunit of a Cullin5 E3 ubiquitin ligase complex. SOCS2 binds to phosphotyrosine-modified epitopes as degrons for ubiquitination and proteasomal degradation, yet the molecular basis of substrate recognition has remained elusive. Here, we report co-crystal structures of SOCS2-ElonginB-ElonginC in complex with phosphorylated peptides from substrates growth hormone receptor (GHR-pY595) and erythropoietin receptor (EpoR-pY426) at 1.98 Å and 2.69 Å, respectively. Both peptides bind in an extended conformation recapitulating the canonical SH2 domain-pY pose, but capture different conformations of the EF loop via specific hydrophobic interactions. The flexible BG loop is fully defined in the electron density, and does not contact the substrate degron directly. Cancer-associated SNPs located around the pY pocket weaken substrate-binding affinity in biophysical assays. Our findings reveal insights into substrate recognition and specificity by SOCS2, and provide a blueprint for small molecule ligand design.

    Organizational Affiliation: 

    Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK. a.ciulli@dundee.ac.uk.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Elongin-B B104Homo sapiensMutation(s): 0 
Gene Names: ELOB, TCEB2
Find proteins for Q15370 (Homo sapiens)
Explore Q15370 
Go to UniProtKB:  Q15370
NIH Common Fund Data Resources
PHAROS:  Q15370
GTEx:  ENSG00000103363
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Elongin-C C97Homo sapiensMutation(s): 0 
Gene Names: ELOC, TCEB1
Find proteins for Q15369 (Homo sapiens)
Explore Q15369 
Go to UniProtKB:  Q15369
NIH Common Fund Data Resources
PHAROS:  Q15369
GTEx:  ENSG00000154582
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Suppressor of cytokine signaling 2 A169Homo sapiensMutation(s): 0 
Gene Names: SOCS2, CIS2, SSI2, STATI2
Find proteins for O14508 (Homo sapiens)
Explore O14508 
Go to UniProtKB:  O14508
NIH Common Fund Data Resources
PHAROS:  O14508
GTEx:  ENSG00000120833
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Erythropoietin receptor D11Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG
Download Ideal Coordinates CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS		BL-PEPTIDE LINKINGC5 H12 As N O2 SCYS
PTR
Query on PTR		DL-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.287α = 90
b = 56.327β = 91.53
c = 203.392γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
AutoPROCdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdomERC-2012-StG-311460 DrugE3CRLs
United KingdomUniversity of Dundee, PhD Scholarship
Wellcome TrustUnited Kingdom100476/Z/12/Z
Wellcome TrustUnited Kingdom094090/Z/10/Z

Revision History 

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Structure summary
  • Version 1.2: 2019-06-19
    Changes: Data collection, Database references