3SE3

human IFNa2-IFNAR ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.251 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural linkage between ligand discrimination and receptor activation by type I interferons.

Thomas, C.Moraga, I.Levin, D.Krutzik, P.O.Podoplelova, Y.Trejo, A.Lee, C.Yarden, G.Vleck, S.E.Glenn, J.S.Nolan, G.P.Piehler, J.Schreiber, G.Garcia, K.C.

(2011) Cell 146: 621-632

  • DOI: https://doi.org/10.1016/j.cell.2011.06.048
  • Primary Citation of Related Structures:  
    3S8W, 3S98, 3S9D, 3SE3, 3SE4

  • PubMed Abstract: 

    Type I Interferons (IFNs) are important cytokines for innate immunity against viruses and cancer. Sixteen human type I IFN variants signal through the same cell-surface receptors, IFNAR1 and IFNAR2, yet they can evoke markedly different physiological effects. The crystal structures of two human type I IFN ternary signaling complexes containing IFNα2 and IFNω reveal recognition modes and heterotrimeric architectures that are unique among the cytokine receptor superfamily but conserved between different type I IFNs. Receptor-ligand cross-reactivity is enabled by conserved receptor-ligand "anchor points" interspersed among ligand-specific interactions that "tune" the relative IFN-binding affinities, in an apparent extracellular "ligand proofreading" mechanism that modulates biological activity. Functional differences between IFNs are linked to their respective receptor recognition chemistries, in concert with a ligand-induced conformational change in IFNAR1, that collectively control signal initiation and complex stability, ultimately regulating differential STAT phosphorylation profiles, receptor internalization rates, and downstream gene expression patterns.


  • Organizational Affiliation

    Howard Hughes Medical Institute, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interferon alpha/beta receptor 1414Homo sapiensMutation(s): 0 
Gene Names: IFNAR1IFNAR
UniProt & NIH Common Fund Data Resources
Find proteins for P17181 (Homo sapiens)
Explore P17181 
Go to UniProtKB:  P17181
PHAROS:  P17181
GTEx:  ENSG00000142166 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17181
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P17181-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Interferon alpha 2b166Homo sapiensMutation(s): 3 
UniProt & NIH Common Fund Data Resources
Find proteins for P01563 (Homo sapiens)
Explore P01563 
Go to UniProtKB:  P01563
PHAROS:  P01563
GTEx:  ENSG00000188379 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01563
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Interferon alpha/beta receptor 2199Homo sapiensMutation(s): 0 
Gene Names: IFNAR2IFNABRIFNARB
UniProt & NIH Common Fund Data Resources
Find proteins for P48551 (Homo sapiens)
Explore P48551 
Go to UniProtKB:  P48551
PHAROS:  P48551
GTEx:  ENSG00000159110 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48551
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.251 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.37α = 90
b = 93.37β = 90
c = 401.5γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2012-03-21
    Changes: Database references
  • Version 1.2: 2013-08-21
    Changes: Structure summary
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary