Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Helical - H  (3D View)
Global Stoichiometry: Hetero 14-mer - A6B4C Pseudo Symmetry: Helical - H  (3D View)
Pseudo Stoichiometry: Homo 14-mer - A14 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 179.46 kDa 
• Atom Count: 11534 
• Residue Count: 1430 
• Unique protein chains: 3

3MOP

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

• DOI: 10.2210/pdb3MOP/pdb

• Classification: SIGNALING PROTEIN, IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-04-23 Released: 2010-06-02 
• Deposition Author(s): Lin, S.-C., Lo, Y.-C., Wu, H.

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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 

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

• PubMed: 20485341 
• DOI: 10.1038/nature09121
• Structures With Same Primary Citation


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Myeloid differentiation primary response protein MyD88	A, B, C, D, E, F	110	Homo sapiens	Mutation(s): 0  Gene Names: MYD88
Find proteins for Q99836 (Homo sapiens) Explore Q99836  Go to UniProtKB:  Q99836
NIH Common Fund Data Resources
PHAROS  Q99836 GTEx  ENSG00000172936

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Interleukin-1 receptor-associated kinase 4	G, H, I, J	113	Homo sapiens	Mutation(s): 0  Gene Names: IRAK4 EC: 2.7.11.1
Find proteins for Q9NWZ3 (Homo sapiens) Explore Q9NWZ3  Go to UniProtKB:  Q9NWZ3
NIH Common Fund Data Resources
PHAROS  Q9NWZ3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Interleukin-1 receptor-associated kinase-like 2	K, L, M, N	111	Homo sapiens	Mutation(s): 1  Gene Names: IRAK2
Find proteins for O43187 (Homo sapiens) Explore O43187  Go to UniProtKB:  O43187
NIH Common Fund Data Resources
PHAROS  O43187 GTEx  ENSG00000134070

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 = 101.709	α = 90
b = 307.116	β = 90
c = 187.619	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-04-23 
• Released Date: 2010-06-02 
Deposition Author(s): Lin, S.-C., Lo, Y.-C., Wu, H.

Revision History 

• 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