3UB2 | pdb_00003ub2

TIR domain of Mal/TIRAP

• PDB DOI: https://doi.org/10.2210/pdb3UB2/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-23 Released: 2012-05-16 
• Deposition Author(s): Shen, Y., Lin, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.262 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Literature

Structural Insights into TIR Domain Specificity of the Bridging Adaptor Mal in TLR4 Signaling

Lin, Z., Lu, J., Zhou, W., Shen, Y.

(2012) PLoS One 7: e34202-e34202

• PubMed: 22485159 
• DOI: https://doi.org/10.1371/journal.pone.0034202
• Primary Citation Related Structures: 
  3UB2, 3UB3, 3UB4


• PubMed Abstract: 
  

  MyD88 adaptor-like protein (Mal) is a crucial adaptor that acts as a bridge to recruit the MyD88 molecule to activated TLR4 receptors in response to invading pathogens. The specific assembly of the Toll/interleukin-1 receptor (TIR) domains of TLR4, Mal and MyD88 is responsible for proper signal transduction in the TLR4 signaling pathway. However, the molecular mechanism for the specificity of these TIR domains remains unclear. Here, we present the crystal structure of the TIR domain of the human Mal molecule (Mal-TIR) at a resolution of 2.4 Å. Unexpectedly, Mal-TIR exhibits an extraordinarily long AB loop, but no αB helix or BB loop, distinguishing it from other TIR domains. More importantly, the Mal-TIR AB loop is capable of mediating direct binding to the TIR domains of TLR4 and MyD88 simultaneously. We also found that Mal-TIR can form a back-to-back dimer that may resemble the dimeric assembly of the entire Mal molecule. Our data demonstrate the bridge role of the Mal-TIR domain and provide important information about TIR domain specificity.

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Organizational Affiliation: 
• State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.12 kDa 
• Atom Count: 990 
• Modeled Residue Count: 125 
• Deposited Residue Count: 146 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll/interleukin-1 receptor domain-containing adapter protein	A	146	Homo sapiens	Mutation(s): 0  Gene Names: TIRAP, MAL
UniProt & NIH Common Fund Data Resources
Find proteins for P58753 (Homo sapiens) Explore P58753  Go to UniProtKB:  P58753
PHAROS:  P58753 GTEx:  ENSG00000150455

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTT	B [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.262 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.508	α = 90
b = 87.508	β = 90
c = 81.684	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-16 
Deposition Author(s): Shen, Y., Lin, Z.

Revision History  

• Version 1.0: 2012-05-16
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary