Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A2B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A3B3C1 

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

Macromolecule Content

• Total Structure Weight: 225.96 kDa 
• Atom Count: 15521 
• Residue Count: 1964 
• Unique protein chains: 7

3ULU

Structure of quaternary complex of human TLR3ecd with three Fabs (Form1)

• DOI: 10.2210/pdb3ULU/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Homo sapiens
• Mutation(s): No 


• Deposited: 2011-11-11 Released: 2012-05-23 
• Deposition Author(s): Luo, J., Gilliland, G.L., Obmolova, O., Malia, T., Teplyakov, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.52 Å
• R-Value Free: 0.309 
• R-Value Work: 0.268 
• R-Value Observed: 0.270 

Literature

Lateral Clustering of TLR3:dsRNA Signaling Units Revealed by TLR3ecd:3Fabs Quaternary Structure.

Luo, J., Obmolova, G., Malia, T.J., Wu, S.J., Duffy, K.E., Marion, J.D., Bell, J.K., Ge, P., Zhou, Z.H., Teplyakov, A., Zhao, Y., Lamb, R.J., Jordan, J.L., San Mateo, L.R., Sweet, R.W., Gilliland, G.L.

(2012) J Mol Biol 421: 112-124

• PubMed: 22579623 
• DOI: 10.1016/j.jmb.2012.05.006
• Primary Citation of Related Structures:  
  3ULS, 3ULU, 3ULV


• PubMed Abstract: 
  

Toll-like receptor 3 (TLR3) recognizes dsRNA and initiates an innate immune response through the formation of a signaling unit (SU) composed of one double-stranded RNA (dsRNA) and two TLR3 molecules. We report the crystal structure of human TLR3 ectodomain (TLR3ecd) in a quaternary complex with three neutralizing Fab fragments. Fab15 binds an epitope that overlaps the C-terminal dsRNA binding site and, in biochemical assays, blocks the interaction of TLR3ecd with dsRNA, thus directly antagonizing TLR3 signaling through inhibition of SU formation. In contrast, Fab12 and Fab1068 bind TLR3ecd at sites distinct from the N- and C-terminal regions that interact with dsRNA and do not inhibit minimal SU formation with short dsRNA. Molecular modeling based on the co-structure rationalizes these observations by showing that both Fab12 and Fab1068 prevent lateral clustering of SUs along the length of the dsRNA ligand. This model is further supported by cell-based assay results using dsRNA ligands of lengths that support single and multiple SUs. Thus, their antagonism of TLR3 signaling indicates that lateral clustering of SUs is required for TLR3 signal transduction.

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Organizational Affiliation: 

Biologics Research, Janssen Research and Development, L.L.C., 145 King of Prussia Road, Radnor, PA 19087, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 3	A	694	Homo sapiens	Mutation(s): 0  Gene Names: TLR3
Find proteins for O15455 (Homo sapiens) Explore O15455  Go to UniProtKB:  O15455
NIH Common Fund Data Resources
PHAROS  O15455 GTEx  ENSG00000164342

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab15 light chain	L	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab15 heavy chain	H	225	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab12 light chain	C	213	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab12 heavy chain	D	226	Homo sapiens	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab1068 light chain	E	215	Homo sapiens	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab1068 heavy chain	F	223	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 8
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, G, I, J	2		N-Glycosylation

Entity ID: 9
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K	4		N-Glycosylation

Entity ID: 10
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	M	3		N-Glycosylation

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.52 Å
• R-Value Free: 0.309 
• R-Value Work: 0.268 
• R-Value Observed: 0.270 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 214.9	α = 90
b = 142.08	β = 103.17
c = 125.04	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-11-11 
• Released Date: 2012-05-23 
Deposition Author(s): Luo, J., Gilliland, G.L., Obmolova, O., Malia, T., Teplyakov, A.

Revision History 

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2012-05-30
  Changes: Database references
• Version 1.2: 2012-07-25
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary