5ZLN

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

• PDB DOI: https://doi.org/10.2210/pdb5ZLN/pdb
• NAKB: 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 

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 193.5 kDa 
• Atom Count: 13,446 
• Modelled Residue Count: 1,532 
• Deposited Residue Count: 1,618 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

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
UniProt
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	Length	2D Diagram	Glycosylation	3D Interactions
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
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	R [auth A], W [auth B], X [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	S [auth A], T [auth A], U [auth A], V [auth A], Y [auth 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

• 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
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary