Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 193.50 kDa 
• Atom Count: 13446 
• Residue Count: 1532 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

5ZLN

Crystal structure of mouse TLR9 in complex with two DNAs (CpG DNA and TCGCCA DNA)

• DOI: 10.2210/pdb5ZLN/pdb
• NDB: 5ZLN

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, synthetic construct
• Expression System: Drosophila melanogaster
• Mutation(s): Yes 


• Deposited: 2018-03-28 Released: 2018-04-25 
• Deposition Author(s): Ishida, H., Ohto, U., Shimizu, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.238 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 

Literature

Structural basis for species-specific activation of mouse Toll-like receptor 9

Ishida, H., Ohto, U., Shibata, T., Miyake, K., Shimizu, T.

(2018) FEBS Lett 592: 2636-2646

• PubMed: 29961984 
• DOI: 10.1002/1873-3468.13176
• Primary Citation of Related Structures:  
  5ZLN


• PubMed Abstract: 
  

Single-stranded DNA containing unmethylated cytosine-phosphate-guanine (CpG) motifs derived from microorganisms are recognized by Toll-like receptor (TLR) 9 and activate an innate immune response. TLR9 has two DNA-binding sites for CpG DNA and DNA containing cytosine at the second position from the 5'-end; both are required for efficient TLR9 activation in most vertebrate species. However, mouse TLR9 can be dimerized by CpG DNA only, although the underlying mechanism remains elusive. Here, we report the crystal structure of mouse TLR9 complexed with both DNAs. Although most TLR9-CpG DNA interactions are conserved among species, some are unique to mice and involved in species-specificity. These findings provide the structural basis for how mouse TLR9 dimerizes efficiently in response to CpG DNA to activate innate immunity.

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Organizational Affiliation: 

Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 9	A, B	793	Mus musculus	Mutation(s): 8  Gene Names: Tlr9
Find proteins for Q9EQU3 (Mus musculus) Explore Q9EQU3  Go to UniProtKB:  Q9EQU3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*GP*CP*GP*TP*TP*TP*TP*T)-3')	C, D	10	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*GP*C)-3')	E, F	6	synthetic construct

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H	3		N-Glycosylation

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, J, K, L, M, N, O, P, Q	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.238 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.306	α = 90
b = 128.141	β = 90
c = 156.798	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-03-28 
• Released Date: 2018-04-25 
Deposition Author(s): Ishida, H., Ohto, U., Shimizu, T.

Revision History 

• Version 1.0: 2018-04-25
  Type: Initial release
  
• Version 1.1: 2018-08-08
  Changes: Data collection, Database references
• Version 1.2: 2018-09-12
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary