1Y6N

Crystal structure of Epstein-Barr virus IL-10 mutant (A87I) complexed with the soluble IL-10R1 chain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Same structure, different function crystal structure of the Epstein-Barr virus IL-10 bound to the soluble IL-10R1 chain.

Yoon, S.I.Jones, B.C.Logsdon, N.J.Walter, M.R.

(2005) Structure 13: 551-564

  • DOI: 10.1016/j.str.2005.01.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human IL-10 (hIL-10) is a cytokine that modulates diverse immune responses. The Epstein-Barr virus (EBV) genome contains an IL-10 homolog (vIL-10) that shares high sequence and structural similarity with hIL-10. Although vIL-10 suppresses inflammator ...

    Human IL-10 (hIL-10) is a cytokine that modulates diverse immune responses. The Epstein-Barr virus (EBV) genome contains an IL-10 homolog (vIL-10) that shares high sequence and structural similarity with hIL-10. Although vIL-10 suppresses inflammatory responses like hIL-10, it cannot activate many other immunostimulatory functions performed by the cellular cytokine. These functional differences have been correlated with the approximately 1000-fold lower affinity of vIL-10, compared to hIL-10, for the IL-10R1 receptor chain. To define the structural basis for these observations, crystal structures of vIL-10 and a vIL-10 point mutant were determined bound to the soluble IL-10R1 receptor fragment (sIL-10R1) at 2.8 and 2.7 A resolution, respectively. The structures reveal that subtle changes in the conformation and dynamics of the vIL-10 AB and CD loops and an orientation change of vIL-10 on sIL-10R1 are the main factors responsible for vIL-10's reduced affinity for sIL-10R1 and its distinct biological profile.


    Organizational Affiliation

    Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Viral interleukin-10 homolog
L
145Epstein-Barr virus (strain B95-8)Mutation(s): 1 
Find proteins for P03180 (Epstein-Barr virus (strain B95-8))
Go to UniProtKB:  P03180
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Interleukin-10 receptor alpha chain
R
214Homo sapiensMutation(s): 6 
Gene Names: IL10RA (IL10R)
Find proteins for Q13651 (Homo sapiens)
Go to Gene View: IL10RA
Go to UniProtKB:  Q13651
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
L
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.206 
  • Space Group: P 32 1 2
Unit Cell:
Length (Å)Angle (°)
a = 45.603α = 90.00
b = 45.603β = 90.00
c = 310.611γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance