Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 43.46 kDa 
• Atom Count: 2782 
• Modelled Residue Count: 356 
• Deposited Residue Count: 381 
• Unique protein chains: 4

6I4X

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

• DOI: 10.2210/pdb6I4X/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-11-12 Released: 2019-05-29 
• Deposition Author(s): Kung, W.W., Ramachandran, S., Makukhin, N., Bruno, E., Ciulli, A.
• Funding Organization(s): European Research Council, Wellcome Trust

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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 

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

• PubMed: 31182716 
• 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 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.

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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. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	A [auth B]	104	Homo sapiens	Mutation(s): 0  Gene Names: ELOB, TCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens) Explore Q15370  Go to UniProtKB:  Q15370
PHAROS:  Q15370 GTEx:  ENSG00000103363

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	B [auth C]	97	Homo sapiens	Mutation(s): 0  Gene Names: ELOC, TCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens) Explore Q15369  Go to UniProtKB:  Q15369
PHAROS:  Q15369 GTEx:  ENSG00000154582

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Suppressor of cytokine signaling 2	C [auth A]	169	Homo sapiens	Mutation(s): 0  Gene Names: SOCS2, CIS2, SSI2, STATI2
UniProt & NIH Common Fund Data Resources
Find proteins for O14508 (Homo sapiens) Explore O14508  Go to UniProtKB:  O14508
PHAROS:  O14508 GTEx:  ENSG00000120833

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Erythropoietin receptor	D	11	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAS	A [auth B]	L-PEPTIDE LINKING	C5 H12 As N O2 S		CYS
PTR	D	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

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 = 41.287	α = 90
b = 56.327	β = 91.53
c = 203.392	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
AutoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-11-12 
• Released Date: 2019-05-29 
Deposition Author(s): Kung, W.W., Ramachandran, S., Makukhin, N., Bruno, E., Ciulli, A.

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Funding Organization	Location	Grant Number
European Research Council	United Kingdom	ERC-2012-StG-311460 DrugE3CRLs
	United Kingdom	University of Dundee, PhD Scholarship
Wellcome Trust	United Kingdom	100476/Z/12/Z
Wellcome Trust	United Kingdom	094090/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