5BO4 image
Deposition Date 2015-05-27
Release Date 2015-07-08
Last Version Date 2024-10-09
Entry Detail
PDB ID:
5BO4
Title:
Structure of SOCS2:Elongin C:Elongin B from DMSO-treated crystals
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
2.90 Å
R-Value Free:
0.28
R-Value Work:
0.22
R-Value Observed:
0.23
Space Group:
P 32
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Suppressor of cytokine signaling 2
Gene (Uniprot):SOCS2
Chain IDs:A, D, G, J, M, P
Chain Length:169
Number of Molecules:6
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor B polypeptide 2
Gene (Uniprot):ELOB
Chain IDs:B, E, H, K, N, Q
Chain Length:104
Number of Molecules:6
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor B polypeptide 1
Gene (Uniprot):ELOC
Chain IDs:C, F, I, L, O, R
Chain Length:97
Number of Molecules:6
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
CAS A CYS modified residue
Primary Citation
Serendipitous SAD Solution for DMSO-Soaked SOCS2-ElonginC-ElonginB Crystals Using Covalently Incorporated Dimethylarsenic: Insights into Substrate Receptor Conformational Flexibility in Cullin RING Ligases.
Plos One 10 e0131218 e0131218 (2015)
PMID: 26121586 DOI: 10.1371/journal.pone.0131218

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures