6E3L

Interferon gamma signalling complex with IFNGR1 and IFNGR2

  • Classification: CYTOKINE
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni, Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2018-07-14 Released: 2019-02-27 
  • Deposition Author(s): Jude, K.M., Mendoza, J.L., Garcia, K.C.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structure of the IFN gamma receptor complex guides design of biased agonists.

Mendoza, J.L.Escalante, N.K.Jude, K.M.Sotolongo Bellon, J.Su, L.Horton, T.M.Tsutsumi, N.Berardinelli, S.J.Haltiwanger, R.S.Piehler, J.Engleman, E.G.Garcia, K.C.

(2019) Nature 567: 56-60

  • DOI: 10.1038/s41586-019-0988-7
  • Primary Citation of Related Structures:  
    6E3K, 6E3L

  • PubMed Abstract: 
  • The cytokine interferon-γ (IFNγ) is a central coordinator of innate and adaptive immunity, but its highly pleiotropic actions have diminished its prospects for use as an immunotherapeutic agent. Here, we took a structure-based approach to decoupling IFNγ pleiotropy ...

    The cytokine interferon-γ (IFNγ) is a central coordinator of innate and adaptive immunity, but its highly pleiotropic actions have diminished its prospects for use as an immunotherapeutic agent. Here, we took a structure-based approach to decoupling IFNγ pleiotropy. We engineered an affinity-enhanced variant of the ligand-binding chain of the IFNγ receptor IFNγR1, which enabled us to determine the crystal structure of the complete hexameric (2:2:2) IFNγ-IFNγR1-IFNγR2 signalling complex at 3.25 Å resolution. The structure reveals the mechanism underlying deficits in IFNγ responsiveness in mycobacterial disease syndrome resulting from a T168N mutation in IFNγR2, which impairs assembly of the full signalling complex. The topology of the hexameric complex offers a blueprint for engineering IFNγ variants to tune IFNγ receptor signalling output. Unexpectedly, we found that several partial IFNγ agonists exhibited biased gene-expression profiles. These biased agonists retained the ability to induce upregulation of major histocompatibility complex class I antigen expression, but exhibited impaired induction of programmed death-ligand 1 expression in a wide range of human cancer cell lines, offering a route to decoupling immunostimulatory and immunosuppressive functions of IFNγ for therapeutic applications.


    Organizational Affiliation

    Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. kcgarcia@stanford.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interferon gammaA, B148Homo sapiensMutation(s): 0 
Gene Names: IFNG
UniProt & NIH Common Fund Data Resources
Find proteins for P01579 (Homo sapiens)
Explore P01579 
Go to UniProtKB:  P01579
PHAROS:  P01579
GTEx:  ENSG00000111537 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01579
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interferon gamma receptor 1C, D242Homo sapiensMutation(s): 6 
Gene Names: IFNGR1
UniProt & NIH Common Fund Data Resources
Find proteins for P15260 (Homo sapiens)
Explore P15260 
Go to UniProtKB:  P15260
PHAROS:  P15260
GTEx:  ENSG00000027697 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15260
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Interferon gamma receptor 2E,
F [auth I]
233Homo sapiensMutation(s): 0 
Gene Names: IFNGR2IFNGT1
UniProt & NIH Common Fund Data Resources
Find proteins for P38484 (Homo sapiens)
Explore P38484 
Go to UniProtKB:  P38484
PHAROS:  P38484
GTEx:  ENSG00000159128 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38484
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth F],
J,
M
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth G],
I [auth H],
K
3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL 6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G34442SS
GlyCosmos:  G34442SS
GlyGen:  G34442SS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 
  • Space Group: P 21 21 21
  • Diffraction Data DOI: 10.15785/SBGRID/592 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.694α = 90
b = 150.212β = 90
c = 212.668γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesRO1-AI51321
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesK01CA175127

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-03-20
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary