7SZL | pdb_00007szl

Crystal structure of the Toll/interleukin-1 receptor domain of human IL-1R10 (IL-1RAPL2)

• PDB DOI: https://doi.org/10.2210/pdb7SZL/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-11-28 Released: 2022-02-02 
• Deposition Author(s): Nimma, S., Gu, W., Manik, M.K., Ve, T., Nanson, J.D., Kobe, B.
• Funding Organization(s): Australian Research Council (ARC), National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.261 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the Toll/interleukin-1 receptor (TIR) domain of IL-1R10 provides structural insights into TIR domain signalling.

Nimma, S., Gu, W., Manik, M.K., Ve, T., Nanson, J.D., Kobe, B.

(2022) FEBS Lett 596: 886-897

• PubMed: 35038778 
• DOI: https://doi.org/10.1002/1873-3468.14288
• Primary Citation Related Structures: 
  7SZL


• PubMed Abstract: 
  

  The Toll/interleukin-1 receptor (TIR) domains are key innate immune signalling modules. Here, we present the crystal structure of the TIR domain of human interleukin-1 receptor 10 (IL-1R10), also called interleukin 1 receptor accessory protein like 2. It is similar to that of IL-1R9 (IL-1RAPL1) but shows significant structural differences to those from Toll-like receptors (TLRs) and the adaptor proteins MyD88 adaptor-like protein (MAL) and MyD88. Interactions of TIR domains in their respective crystals and the higher-order assemblies (MAL and MyD88) reveal the presence of a common 'BCD surface', suggesting its functional significance. We also show that the TIR domains of IL-1R10 and IL-1R9 lack NADase activity, consistent with their structures. Our study provides a foundation for unravelling the functions of IL-1R9 and IL-1R10.

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Organizational Affiliation: 
• School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute of Molecular Bioscience, The University of Queensland, Brisbane, Australia.
Institute for Glycomics, Griffith University, Southport, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 18.92 kDa 
• Atom Count: 1,285 
• Modeled Residue Count: 154 
• Deposited Residue Count: 160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
X-linked interleukin-1 receptor accessory protein-like 2	A	160	Homo sapiens	Mutation(s): 0  Gene Names: IL1RAPL2, IL1R9 EC: 3.2.2.6
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NP60 (Homo sapiens) Explore Q9NP60  Go to UniProtKB:  Q9NP60
PHAROS:  Q9NP60 GTEx:  ENSG00000189108

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.261 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.655	α = 90
b = 50.655	β = 90
c = 181.967	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): Nimma, S., Gu, W., Manik, M.K., Ve, T., Nanson, J.D., Kobe, B.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	FL180100109, FT200100572
National Health and Medical Research Council (NHMRC, Australia)	Australia	1107804, 1160570, 1071659

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 1.1: 2022-04-20
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description