Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A2BCDEF Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer -A3B3C 

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

Macromolecule Content

• Total Structure Weight: 226123.58 
• Atom Count: 15521 
• Residue Count: 2010 
• 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: Homo sapiens, Spodoptera frugiperda


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

---

Experimental Data Snapshot

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

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:  
  3ULV, 3ULS


• 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.

---

Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Toll-like receptor 3	A	694	Homo sapiens	Mutation(s): 0  Gene Names: TLR3
Find proteins for O15455 (Homo sapiens) Go to Gene View: TLR3 Go to UniProtKB:  O15455

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Fab15 light chain	L	214	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Fab15 heavy chain	H	225	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Fab12 light chain	C	213	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
Fab12 heavy chain	D	226	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
Fab1068 light chain	E	215	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
Fab1068 heavy chain	F	223	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 214.900	α = 90.00
b = 142.080	β = 103.17
c = 125.040	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
StructureStudio	data collection
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
  Type: Database references
• Version 1.2: 2012-07-25
  Type: Database references