3MOP

The ternary Death Domain complex of MyD88, IRAK4, and IRAK2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Helical assembly in the MyD88-IRAK4-IRAK2 complex in TLR/IL-1R signalling.

Lin, S.C., Lo, Y.C., Wu, H.

(2010) Nature 465: 885-890

  • DOI: 10.1038/nature09121
  • Primary Citation of Related Structures:  
    3MOP

  • PubMed Abstract: 

    • MyD88, IRAK4 and IRAK2 are critical signalling mediators of the TLR/IL1-R superfamily. Here we report the crystal structure of the MyD88-IRAK4-IRAK2 death domain (DD) complex, which surprisingly reveals a left-handed helical oligomer that consists of 6 MyD88, 4 IRAK4 and 4 IRAK2 DDs ...

    MyD88, IRAK4 and IRAK2 are critical signalling mediators of the TLR/IL1-R superfamily. Here we report the crystal structure of the MyD88-IRAK4-IRAK2 death domain (DD) complex, which surprisingly reveals a left-handed helical oligomer that consists of 6 MyD88, 4 IRAK4 and 4 IRAK2 DDs. Assembly of this helical signalling tower is hierarchical, in which MyD88 recruits IRAK4 and the MyD88-IRAK4 complex recruits the IRAK4 substrates IRAK2 or the related IRAK1. Formation of these Myddosome complexes brings the kinase domains of IRAKs into proximity for phosphorylation and activation. Composite binding sites are required for recruitment of the individual DDs in the complex, which are confirmed by mutagenesis and previously identified signalling mutations. Specificities in Myddosome formation are dictated by both molecular complementarity and correspondence of surface electrostatics. The MyD88-IRAK4-IRAK2 complex provides a template for Toll signalling in Drosophila and an elegant mechanism for versatile assembly and regulation of DD complexes in signal transduction.

    Organizational Affiliation: 

    Department of Biochemistry, Weill Cornell Medical College, New York, New York 10021, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Myeloid differentiation primary response protein MyD88
A, B, C, D, E, F
A, B, C, D, E, F
110Homo sapiensMutation(s): 0 
Gene Names: MYD88
UniProt & NIH Common Fund Data Resources
Find proteins for Q99836 (Homo sapiens)
Explore Q99836 
Go to UniProtKB:  Q99836
PHAROS:  Q99836
GTEx:  ENSG00000172936 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99836
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 receptor-associated kinase 4G, H, I, J113Homo sapiensMutation(s): 0 
Gene Names: IRAK4
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWZ3 (Homo sapiens)
Explore Q9NWZ3 
Go to UniProtKB:  Q9NWZ3
PHAROS:  Q9NWZ3
GTEx:  ENSG00000198001 
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UniProt GroupQ9NWZ3
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 receptor-associated kinase-like 2K, L, M, N111Homo sapiensMutation(s): 1 
Gene Names: IRAK2
UniProt & NIH Common Fund Data Resources
Find proteins for O43187 (Homo sapiens)
Explore O43187 
Go to UniProtKB:  O43187
PHAROS:  O43187
GTEx:  ENSG00000134070 
Entity Groups  
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UniProt GroupO43187
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.709α = 90
b = 307.116β = 90
c = 187.619γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description