1Y6M | pdb_00001y6m

Crystal structure of Epstein-Barr virus IL-10 complexed with the soluble IL-10R1 chain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.315 (Depositor), 0.308 (DCC) 
  • R-Value Work: 
    0.261 (Depositor), 0.257 (DCC) 
  • R-Value Observed: 
    0.264 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1Y6M

This is version 1.4 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: https://doi.org/10.1016/j.str.2005.01.016
  • Primary Citation Related Structures: 
    1Y6K, 1Y6M, 1Y6N

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 41.67 kDa 
  • Atom Count: 2,833 
  • Modeled Residue Count: 346 
  • Deposited Residue Count: 359 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Viral interleukin-10 homologA [auth L]145human gammaherpesvirus 4Mutation(s): 0 
Gene Names: BCRF1
UniProt
Find proteins for P03180 (Epstein-Barr virus (strain B95-8))
Explore P03180 
Go to UniProtKB:  P03180
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03180
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-10 receptor alpha chainB [auth R]214Homo sapiensMutation(s): 6 
Gene Names: IL10RAIL10R
UniProt & NIH Common Fund Data Resources
Find proteins for Q13651 (Homo sapiens)
Explore Q13651 
Go to UniProtKB:  Q13651
PHAROS:  Q13651
GTEx:  ENSG00000110324 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13651
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.315 (Depositor), 0.308 (DCC) 
  • R-Value Work:  0.261 (Depositor), 0.257 (DCC) 
  • R-Value Observed: 0.264 (Depositor) 
Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.121α = 90
b = 47.121β = 90
c = 300.708γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references
  • Version 1.4: 2024-10-30
    Changes: Data collection, Structure summary