6BXC

Crystal structure of N-terminal fragment of Zebrafish Toll-Like Receptor 5 (TLR5) with Lamprey Variable Lymphocyte Receptor 9 (VLR9) bound

• PDB DOI: https://doi.org/10.2210/pdb6BXC/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Danio rerio, Eptatretus burgeri, Petromyzon marinus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2017-12-18 Released: 2018-05-09 
• Deposition Author(s): Gunn, R.J., Wilson, I.A., Cooper, M.D., Herrin, B.R.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.270 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration, light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 142.06 kDa 
• Atom Count: 9,515 
• Modelled Residue Count: 1,213 
• Deposited Residue Count: 1,266 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 5b, Variable lymphocyte receptor B chimera	A, B	455	Danio rerio, Eptatretus burgeri This entity is chimeric	Mutation(s): 0  Gene Names: tlr5b, VLRB
UniProt
Find proteins for Q4G1L2 (Eptatretus burgeri) Explore Q4G1L2  Go to UniProtKB:  Q4G1L2
Find proteins for F8W3J5 (Danio rerio) Explore F8W3J5  Go to UniProtKB:  F8W3J5
UniProt Groups	F8W3J5Q4G1L2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Variable Lymphocyte Receptor 9 (VLR9)	C [auth D], D [auth C]	178	Petromyzon marinus	Mutation(s): 0

Oligosaccharides

Help

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	E	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	F [auth A], G [auth A], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	I [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.270 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.38	α = 112.14
b = 69.413	β = 104.12
c = 84.561	γ = 100.81

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-09 
Deposition Author(s): Gunn, R.J., Wilson, I.A., Cooper, M.D., Herrin, B.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	A1042266
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI072435

Revision History  

• Version 1.0: 2018-05-09
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2022-03-23
  Changes: Author supporting evidence, Database references, Structure summary
• Version 2.2: 2023-10-04
  Changes: Data collection, Refinement description