5T5W

Structure of an affinity matured lambda-IFN/IFN-lambdaR1/IL-10Rbeta receptor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.7 of the entry. See complete history


Literature

The IFN-lambda-IFN-lambda R1-IL-10R beta Complex Reveals Structural Features Underlying Type III IFN Functional Plasticity.

Mendoza, J.L.Schneider, W.M.Hoffmann, H.H.Vercauteren, K.Jude, K.M.Xiong, A.Moraga, I.Horton, T.M.Glenn, J.S.de Jong, Y.P.Rice, C.M.Garcia, K.C.

(2017) Immunity 46: 379-392

  • DOI: 10.1016/j.immuni.2017.02.017
  • Primary Citation of Related Structures:  
    5T5W

  • PubMed Abstract: 
  • Type III interferons (IFN-λs) signal through a heterodimeric receptor complex composed of the IFN-λR1 subunit, specific for IFN-λs, and interleukin-10Rβ (IL-10Rβ), which is shared by multiple cytokines in the IL-10 superfamily. Low affinity of IL-10Rβ for cytokines has impeded efforts aimed at crystallizing cytokine-receptor complexes ...

    Type III interferons (IFN-λs) signal through a heterodimeric receptor complex composed of the IFN-λR1 subunit, specific for IFN-λs, and interleukin-10Rβ (IL-10Rβ), which is shared by multiple cytokines in the IL-10 superfamily. Low affinity of IL-10Rβ for cytokines has impeded efforts aimed at crystallizing cytokine-receptor complexes. We used yeast surface display to engineer a higher-affinity IFN-λ variant, H11, which enabled crystallization of the ternary complex. The structure revealed that IL-10Rβ uses a network of tyrosine residues as hydrophobic anchor points to engage IL-10 family cytokines that present complementary hydrophobic binding patches, explaining its role as both a cross-reactive but cytokine-specific receptor. H11 elicited increased anti-proliferative and antiviral activities in vitro and in vivo. In contrast, engineered higher-affinity type I IFNs did not increase antiviral potency over wild-type type I IFNs. Our findings provide insight into cytokine recognition by the IL-10R family and highlight the plasticity of type III interferon signaling and its therapeutic potential.


    Organizational Affiliation

    Howard Hughes Medical Institute, Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: kcgarcia@stanford.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-10 receptor subunit beta A214Homo sapiensMutation(s): 5 
Gene Names: IL10RBCRFB4D21S58D21S66
Find proteins for Q08334 (Homo sapiens)
Explore Q08334 
Go to UniProtKB:  Q08334
NIH Common Fund Data Resources
PHAROS:  Q08334
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interferon lambda receptor 1 B218Homo sapiensMutation(s): 0 
Gene Names: IFNLR1IL28RALICR2
Find proteins for Q8IU57 (Homo sapiens)
Explore Q8IU57 
Go to UniProtKB:  Q8IU57
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PHAROS:  Q8IU57
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Interferon lambda-3 C176Homo sapiensMutation(s): 4 
Gene Names: IFNL3IL28BIL28CZCYTO22
Find proteins for Q8IZI9 (Homo sapiens)
Explore Q8IZI9 
Go to UniProtKB:  Q8IZI9
NIH Common Fund Data Resources
PHAROS:  Q8IZI9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 31 2 1
  • Diffraction Data DOI: 10.15785/SBGRID/416 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.79α = 90
b = 106.79β = 90
c = 129.71γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1U19AI109662

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 1.2: 2017-08-09
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.4: 2018-08-15
    Changes: Data collection, Database references
  • Version 1.5: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.6: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.7: 2021-03-24
    Changes: Source and taxonomy, Structure summary