Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.67 kDa 
• Atom Count: 2833 
• Modelled Residue Count: 346 
• Deposited Residue Count: 359 
• Unique protein chains: 2

1Y6M

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

• PDB DOI: 10.2210/pdb1Y6M/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Human gammaherpesvirus 4, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Drosophila melanogaster
• Mutation(s): Yes 


• Deposited: 2004-12-06 Released: 2005-05-03 
• Deposition Author(s): Yoon, S.I., Jones, B.C., Logsdon, N.J., Walter, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.315 
• R-Value Work: 0.261 
• R-Value Observed: 0.264 

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

• PubMed: 15837194 
• DOI: 10.1016/j.str.2005.01.016
• Primary Citation of 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Viral interleukin-10 homolog	A [auth L]	145	Human gammaherpesvirus 4	Mutation(s): 0  Gene Names: BCRF1
UniProt
Find proteins for P03180 (Epstein-Barr virus (strain B95-8)) Explore P03180  Go to UniProtKB:  P03180

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-10 receptor alpha chain	B [auth R]	214	Homo sapiens	Mutation(s): 6  Gene Names: IL10RA, IL10R
UniProt & NIH Common Fund Data Resources
Find proteins for Q13651 (Homo sapiens) Explore Q13651  Go to UniProtKB:  Q13651
PHAROS:  Q13651

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.315 
• R-Value Work: 0.261 
• R-Value Observed: 0.264 
• Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.121	α = 90
b = 47.121	β = 90
c = 300.708	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-12-06 
• Released Date: 2005-05-03 
Deposition Author(s): Yoon, S.I., Jones, B.C., Logsdon, N.J., Walter, M.R.

Revision History  

• 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