3W3G

Crystal structure of human TLR8 (unliganded form)

• PDB DOI: https://doi.org/10.2210/pdb3W3G/pdb

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


• Deposited: 2012-12-21 Released: 2013-04-03 
• Deposition Author(s): Tanji, H., Ohto, U., Shimizu, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.236 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 

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: 191.33 kDa 
• Atom Count: 12,865 
• Modelled Residue Count: 1,495 
• Deposited Residue Count: 1,622 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 8	A, B	811	Homo sapiens	Mutation(s): 0  Gene Names: TLR8, UNQ249/PRO286
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NR97 (Homo sapiens) Explore Q9NR97  Go to UniProtKB:  Q9NR97
PHAROS:  Q9NR97 GTEx:  ENSG00000101916

Oligosaccharides

Help

Entity ID: 2
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	C, D, E, G, H	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	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	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], P [auth B], Q [auth B], R [auth B], S [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BU3	O [auth A]	(R,R)-2,3-BUTANEDIOL C4 H10 O2 OWBTYPJTUOEWEK-QWWZWVQMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.236 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.525	α = 90
b = 101.97	β = 104.75
c = 141.34	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Tanji, H., Ohto, U., Shimizu, T.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary