4QDH

Crystal Structure of the C-terminal Domain of Mouse TLR9


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 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

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

Collins, B.Wilson, I.A.

(2014) Proteins 82: 2874-2878

  • DOI: https://doi.org/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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Variable lymphocyte receptor B, Toll-like receptor 9 chimera
A, B
438Eptatretus burgeriMus musculusMutation(s): 0 
Gene Names: Tlr9VLRB
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9EQU3Q4G1L2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
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
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
Q [auth B]
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 = 106.025α = 90
b = 106.025β = 90
c = 221.549γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary