7ZG0 | pdb_00007zg0

Murine IL-27 in complex with IL-27Ra and a non-competing Nb


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 
    0.278 (Depositor), 0.286 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.257 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural basis of activation and antagonism of receptor signaling mediated by interleukin-27.

Skladanowska, K.Bloch, Y.Strand, J.White, K.F.Hua, J.Aldridge, D.Welin, M.Logan, D.T.Soete, A.Merceron, R.Murphy, C.Provost, M.Bazan, J.F.Hunter, C.A.Hill, J.A.Savvides, S.N.

(2022) Cell Rep 41: 111490-111490

  • DOI: https://doi.org/10.1016/j.celrep.2022.111490
  • Primary Citation Related Structures: 
    7ZG0, 7ZXK

  • PubMed Abstract: 

    Interleukin-27 (IL-27) uniquely assembles p28 and EBI3 subunits to a heterodimeric cytokine that signals via IL-27Rα and gp130. To provide the structural framework for receptor activation by IL-27 and its emerging therapeutic targeting, we report here crystal structures of mouse IL-27 in complex with IL-27Rα and of human IL-27 in complex with SRF388, a monoclonal antibody undergoing clinical trials with oncology indications. One face of the helical p28 subunit interacts with EBI3, while the opposite face nestles into the interdomain elbow of IL-27Rα to juxtapose IL-27Rα to EBI3. This orients IL-27Rα for paired signaling with gp130, which only uses its immunoglobulin domain to bind to IL-27. Such a signaling complex is distinct from those mediated by IL-12 and IL-23. The SRF388 binding epitope on IL-27 overlaps with the IL-27Rα interaction site explaining its potent antagonistic properties. Collectively, our findings will facilitate the mechanistic interrogation, engineering, and therapeutic targeting of IL-27.


  • Organizational Affiliation
    • Unit for Structural Biology, Department of Biochemistry and Microbiology Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium.

Macromolecule Content 

  • Total Structure Weight: 195.87 kDa 
  • Atom Count: 10,641 
  • Modeled Residue Count: 1,330 
  • Deposited Residue Count: 1,744 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-27 subunit alpha
A, B
246Mus musculusMutation(s): 0 
Gene Names: Il27Il27a
UniProt & NIH Common Fund Data Resources
Find proteins for Q8K3I6 (Mus musculus)
Explore Q8K3I6 
Go to UniProtKB:  Q8K3I6
IMPC:  MGI:2384409
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8K3I6
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q8K3I6-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-27 subunit beta
C, D
241Mus musculusMutation(s): 0 
Gene Names: Ebi3Il27b
UniProt
Find proteins for O35228 (Mus musculus)
Explore O35228 
Go to UniProtKB:  O35228
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO35228
Glycosylation
Glycosylation Sites: 1Go to GlyGen: O35228-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-27 receptor subunit alpha
E, F
219Mus musculusMutation(s): 0 
Gene Names: Il27raTccrWsx1
UniProt
Find proteins for O70394 (Mus musculus)
Explore O70394 
Go to UniProtKB:  O70394
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO70394
Glycosylation
Glycosylation Sites: 1Go to GlyGen: O70394-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody 5
G, H
166Lama glamaMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, J
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free:  0.278 (Depositor), 0.286 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.257 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.242α = 90
b = 137.707β = 117.49
c = 111.479γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)BelgiumG0E1516N
Research Foundation - Flanders (FWO)BelgiumG0B4918N
Research Foundation - Flanders (FWO)Belgium12S0519N
H2020 Marie Curie Actions of the European CommissionEuropean Union--
Research Foundation - Flanders (FWO)BelgiumHercules

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary