5BO4

Structure of SOCS2:Elongin C:Elongin B from DMSO-treated crystals

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Serendipitous SAD Solution for DMSO-Soaked SOCS2-ElonginC-ElonginB Crystals Using Covalently Incorporated Dimethylarsenic: Insights into Substrate Receptor Conformational Flexibility in Cullin RING Ligases.

Gadd, M.S., Bulatov, E., Ciulli, A.

(2015) Plos One 10: e0131218-e0131218

  • DOI: 10.1371/journal.pone.0131218

  • PubMed Abstract: 

    • Suppressor of cytokine signalling 2 (SOCS2) is the substrate-binding component of a Cullin-RING E3 ubiquitin ligase (CRL) complex that targets phosphorylated hormone receptors for degradation by the ubiquitin-proteasome system. As a key regulator of ...

    Suppressor of cytokine signalling 2 (SOCS2) is the substrate-binding component of a Cullin-RING E3 ubiquitin ligase (CRL) complex that targets phosphorylated hormone receptors for degradation by the ubiquitin-proteasome system. As a key regulator of the transcriptional response to growth signals, SOCS2 and its protein complex partners are potential targets for small molecule development. We found that crystals of SOCS2 in complex with its adaptor proteins, Elongin C and Elongin B, underwent a change in crystallographic parameters when treated with dimethyl sulfoxide during soaking experiments. To solve the phase problem for the new crystal form we identified the presence of arsenic atoms in the crystals, a result of covalent modification of cysteines by cacodylate, and successfully extracted anomalous signal from these atoms for experimental phasing. The resulting structure provides a means for solving future structures where the crystals must be treated with DMSO for ligand soaking approaches. Additionally, the conformational changes induced in this structure reveal flexibility within SOCS2 that match those postulated by previous molecular dynamics simulations. This conformational flexibility illustrates how SOCS2 can orient its substrates for successful ubiquitination by other elements of the CRL complex.

    Organizational Affiliation: 

    Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Suppressor of cytokine signaling 2
A, D, G, J, M, P
169Homo sapiensMutation(s): 0 
Gene Names: SOCS2 (CIS2, SSI2, STATI2)
Find proteins for O14508 (Homo sapiens)
Go to Gene View: SOCS2
Go to UniProtKB:  O14508
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor B polypeptide 2
B, E, H, K, N, Q
104Homo sapiensMutation(s): 0 
Gene Names: ELOB (TCEB2)
Find proteins for Q15370 (Homo sapiens)
Go to Gene View: ELOB
Go to UniProtKB:  Q15370
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor B polypeptide 1
C, F, I, L, O, R
97Homo sapiensMutation(s): 0 
Gene Names: ELOC (TCEB1)
Find proteins for Q15369 (Homo sapiens)
Go to Gene View: ELOC
Go to UniProtKB:  Q15369
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS
A, B, D, E, G, H, J, K, M, N, P, Q
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.229 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 185.217α = 90.00
b = 185.217β = 90.00
c = 67.204γ = 120.00
Software Package:
Software NamePurpose
SOLVEphasing
REFMACrefinement
RESOLVEmodel building
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council--

Revision History 

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Data collection