Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 100.53 kDa 
• Atom Count: 6532 
• Modelled Residue Count: 795 
• Deposited Residue Count: 876 
• Unique protein chains: 1

4QDH

Crystal Structure of the C-terminal Domain of Mouse TLR9

• PDB DOI: 10.2210/pdb4QDH/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Eptatretus burgeri, Mus musculus
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2014-05-13 Released: 2014-06-11 
• Deposition Author(s): Collins, B.C., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.247 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

Literature

Crystal structure of the C-terminal domain of mouse TLR9.

Collins, B., Wilson, I.A.

(2014) Proteins 82: 2874-2878

• PubMed: 24888966 
• DOI: 10.1002/prot.24616
• Primary Citation of Related Structures:  
  4QDH


• PubMed Abstract: 
  

Toll-like receptors (TLRs) are important pattern recognition receptors that function in innate immunity. Elucidating the structure and signaling mechanisms of TLR9, a sensor of foreign and endogenous DNA, is essential for understanding its key role in immunity against microbial pathogens as well as in autoimmunity. Abundant evidence suggests that the TLR9-CTD (C-terminal domain) by itself is capable of DNA binding and signaling. The crystal structure of unliganded mouse TLR9-CTD is presented. TLR9-CTD exhibits one unique feature, a cluster of stacked aromatic and arginine side chains on its concave face. Overall, its structure is most related to the TLR8-CTD, suggesting a similar mode of ligand binding and signaling.

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Organizational Affiliation: 

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Variable lymphocyte receptor B, Toll-like receptor 9 chimera	A, B	438	Eptatretus burgeri, Mus musculus	Mutation(s): 0  Gene Names: Tlr9, VLRB
UniProt
Find proteins for Q4G1L2 (Eptatretus burgeri) Explore Q4G1L2  Go to UniProtKB:  Q4G1L2
Find proteins for Q9EQU3 (Mus musculus) Explore Q9EQU3  Go to UniProtKB:  Q9EQU3
UniProt Groups	Q4G1L2Q9EQU3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	H [auth A], I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B], S [auth B], T [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.247 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.025	α = 90
b = 106.025	β = 90
c = 221.549	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-13 
• Released Date: 2014-06-11 
Deposition Author(s): Collins, B.C., Wilson, I.A.

Revision History  

• Version 1.0: 2014-06-11
  Type: Initial release
  
• Version 1.1: 2014-07-02
  Changes: Database references
• Version 1.2: 2014-10-08
  Changes: Database references
• Version 1.3: 2017-07-26
  Changes: Refinement description, Source and taxonomy
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary