1EVS | pdb_00001evs

CRYSTAL STRUCTURE OF HUMAN ONCOSTATIN M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.261 (Depositor) 
  • R-Value Work: 
    0.205 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Crystal structure and functional dissection of the cytostatic cytokine oncostatin M.

Deller, M.C.Hudson, K.R.Ikemizu, S.Bravo, J.Jones, E.Y.Heath, J.K.

(2000) Structure 8: 863-874

  • DOI: https://doi.org/10.1016/s0969-2126(00)00176-3
  • Primary Citation Related Structures: 
    1EVS

  • PubMed Abstract: 

    The cytokine oncostatin M (OSM) inhibits growth of certain tumour-derived cells, induces proliferation in other cell types (e.g. haemangioblasts) and is a mediator of inflammatory responses. Its mechanism of action is via specific binding to gp130 and either the leukaemia inhibitory factor receptor (LIFR) or oncostatin M receptor (OSMR) systems at the cell surface to form an active signalling complex. We report here the crystal structure of human oncostatin M (hOSM) along with mutagenesis data which map the receptor-binding epitopes of the molecule. The structure was determined to a resolution of 2.2 A and conforms to the haematopoietin cytokine up-up-down-down four-helix bundle topology. The site 2 epitope, responsible for gp130 binding, is centred around Gly120 which forms a 'dimple' on the surface of the molecule located on helices A and C. The site 3 motif, responsible for LIFR and OSMR binding, consists of a protruding Phe160/Lys163 pair located at the start of helix D. The data presented allow functional dissection of the receptor-binding interfaces to atomic resolution. Modelling suggests that the gp130 residue Phe169 packs into the site 2 dimple in an analogous fashion to structurally equivalent residues at the growth hormone-growth hormone receptor interface, implying that certain key features may underlie recognition across the whole cytokine/receptor superfamily. Conversely, detailed comparison of the available structures suggests that variations on a common theme dictate the specificity of receptor-ligand interactions within the gp130 family of cytokines.


  • Organizational Affiliation
    • Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, UK.

Macromolecule Content 

  • Total Structure Weight: 21.14 kDa 
  • Atom Count: 1,435 
  • Modeled Residue Count: 163 
  • Deposited Residue Count: 187 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ONCOSTATIN M187Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P13725 (Homo sapiens)
Explore P13725 
Go to UniProtKB:  P13725
PHAROS:  P13725
GTEx:  ENSG00000099985 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13725
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.261 (Depositor) 
  • R-Value Work:  0.205 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.887α = 90
b = 53.285β = 90
c = 106.694γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-09-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 1.4: 2024-10-30
    Changes: Data collection, Database references, Structure summary