6KN9

Crystal structure of human interleukin 18 receptor beta extracellular domain in complex with an antagonistic scFv


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

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This is version 2.0 of the entry. See complete history


Literature

A Synthetic Human Antibody Antagonizes IL-18R beta Signaling Through an Allosteric Mechanism.

Liu, S.Miersch, S.Li, P.Bai, B.X,Liu, C.C.Qin, W.M.Su, J.Huang, H.M.Pan, J.Sidhu, S.S.Wu, D.H.

(2020) J Mol Biol 432: 1169-1182

  • DOI: 10.1016/j.jmb.2020.01.012
  • Primary Citation of Related Structures:  
    6KN9

  • PubMed Abstract: 
  • The interleukin-18 subfamily belongs to the interleukin-1 family and plays an important role in modulating innate and adaptive immune responses. Dysregulation of IL-18 has been implicated in or correlated with numerous diseases, including inflammatory diseases, autoimmune disorders, and cancer ...

    The interleukin-18 subfamily belongs to the interleukin-1 family and plays an important role in modulating innate and adaptive immune responses. Dysregulation of IL-18 has been implicated in or correlated with numerous diseases, including inflammatory diseases, autoimmune disorders, and cancer. Thus, blockade of IL-18 signaling may offer therapeutic benefits in many pathological settings. Here, we report the development of synthetic human antibodies that target human IL-18Rβ and block IL-18-mediated IFN-γ secretion by inhibiting NF-κB and MAPK dependent pathways. The crystal structure of a potent antagonist antibody in complex with IL-18Rβ revealed inhibition through an unexpected allosteric mechanism. Our findings offer a novel means for therapeutic intervention in the IL-18 pathway and may provide a new strategy for targeting cytokine receptors.


    Organizational Affiliation

    Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China. Electronic address: wudh@shanghaitech.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-18 receptor accessory proteinA, B, C337Homo sapiensMutation(s): 0 
Gene Names: IL18RAPIL1R7
EC: 3.2.2.6
UniProt & NIH Common Fund Data Resources
Find proteins for O95256 (Homo sapiens)
Explore O95256 
Go to UniProtKB:  O95256
PHAROS:  O95256
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
scFvD, E, F257Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
H [auth A], I [auth C]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: 3.30 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.16α = 90
b = 163.16β = 90
c = 64.145γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-08-05 
  • Released Date: 2020-02-12 
  • Deposition Author(s): Wu, D.H., Liu, C.C.

Funding OrganizationLocationGrant Number
National Science Foundation (China)China81572698
National Science Foundation (China)China31771006

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary