6NIH

Crystal structure of human TLR1

• PDB DOI: https://doi.org/10.2210/pdb6NIH/pdb

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


• Deposited: 2018-12-27 Released: 2019-04-17 
• Deposition Author(s): Su, L., Zhang, H.
• 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: 2.30 Å
• R-Value Free: 0.274 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 127.26 kDa 
• Atom Count: 8,757 
• Modelled Residue Count: 1,039 
• Deposited Residue Count: 1,090 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 1,Variable lymphocyte receptor B	A, B	545	Homo sapiens, Eptatretus stoutii This entity is chimeric	Mutation(s): 0  Gene Names: TLR1, KIAA0012, VLRB
UniProt & NIH Common Fund Data Resources
Find proteins for Q2YDZ3 (Eptatretus stoutii) Explore Q2YDZ3  Go to UniProtKB:  Q2YDZ3
Find proteins for Q15399 (Homo sapiens) Explore Q15399  Go to UniProtKB:  Q15399
PHAROS:  Q15399 GTEx:  ENSG00000174125
UniProt Groups	Q2YDZ3Q15399

Oligosaccharides

Help

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

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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47362BJ GlyCosmos:  G47362BJ GlyGen:  G47362BJ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth B], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017	E	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.274 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.028	α = 90
b = 74.377	β = 96.97
c = 106.076	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Currently 6NIH does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-17 
Deposition Author(s): Su, L., Zhang, H.

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

Revision History  

• Version 1.0: 2019-04-17
  Type: Initial release
  
• Version 1.1: 2020-01-01
  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: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary