8SUF

The complex of TOL-1 ectodomain bound to LAT-1 Lectin domain

• PDB DOI: https://doi.org/10.2210/pdb8SUF/pdb

• Classification: CELL ADHESION
• Organism(s): Caenorhabditis elegans
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2023-05-12 Released: 2024-05-15 
• Deposition Author(s): Carmona Rosas, G., Li, J., Arac, D., Ozkan, E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 0.338 
• R-Value Work: 0.288 
• R-Value Observed: 0.291 

Starting Model: in silico

Literature

Structural basis and functional roles for Toll-like receptor binding to Latrophilin adhesion-GPCR in embryo development

Carmona Rosas, G., Li, J., Smith, J.S., Cheng, S., Baltrusaitis, E., Nawrocka, W.I., Zhao, M., Kratsios, P., Arac, D., Ozkan, E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 507.34 kDa 
• Atom Count: 32,993 
• Modelled Residue Count: 4,180 
• Deposited Residue Count: 4,484 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TIR domain-containing protein	A, B, C, D	1,007	Caenorhabditis elegans	Mutation(s): 0  Gene Names: tol-1, C07F11.1, CELE_C07F11.1
UniProt
Find proteins for Q9N5Z3 (Caenorhabditis elegans) Explore Q9N5Z3  Go to UniProtKB:  Q9N5Z3
Glycosylation
Glycosylation Sites: 6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Latrophilin-like protein 1	E, F, G, H	114	Caenorhabditis elegans	Mutation(s): 0  Gene Names: lat-1, B0457.1
UniProt
Find proteins for G5EDW2 (Caenorhabditis elegans) Explore G5EDW2  Go to UniProtKB:  G5EDW2

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	I, M	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC GlyCosmos:  G22573RC GlyGen:  G22573RC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, K, N, O, R	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[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	P	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Entity ID: 7
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	Q	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth D], BA [auth D], S [auth A], T [auth A], U [auth A], V [auth B], W [auth B], X [auth B], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 0.338 
• R-Value Work: 0.288 
• R-Value Observed: 0.291 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.152	α = 90
b = 316.755	β = 90.16
c = 172.441	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-15 
Deposition Author(s): Carmona Rosas, G., Li, J., Arac, D., Ozkan, E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM148412

Revision History  

• Version 1.0: 2024-05-15
  Type: Initial release