5ZSL

Crystal structure of monkey TLR7 in complex with GGUUGG

• PDB DOI: https://doi.org/10.2210/pdb5ZSL/pdb
• NAKB: 5ZSL

• Classification: IMMUNE SYSTEM
• Organism(s): Macaca mulatta, synthetic construct
• Expression System: Drosophila melanogaster
• Mutation(s): Yes 


• Deposited: 2018-04-28 Released: 2019-01-30 
• Deposition Author(s): Zhang, Z., Ohto, U., Shimizu, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.258 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 198.85 kDa 
• Atom Count: 13,046 
• Modelled Residue Count: 1,558 
• Deposited Residue Count: 1,658 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 7	A [auth B], B [auth A]	823	Macaca mulatta	Mutation(s): 4  Gene Names: TLR7
UniProt
Find proteins for B3Y653 (Macaca mulatta) Explore B3Y653  Go to UniProtKB:  B3Y653

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*UP*GP*A)-3')	C [auth D], D [auth E]	6	synthetic construct

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 [auth C], F, G, H	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9K9	T [auth B], U [auth B]	2-amino-9-[(2S,3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]-3,9-dihydro-6H-purin-6-one C10 H12 N5 O7 P UASRYODFRYWBRC-UUOKFMHZSA-N
NAG	I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], V [auth A], W [auth A], X [auth A], Y [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	AA [auth A], BA [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], Z [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.258 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.63	α = 90
b = 139.424	β = 90
c = 150.893	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-30 
Deposition Author(s): Zhang, Z., Ohto, U., Shimizu, T.

Revision History  

• Version 1.0: 2019-01-30
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-03-13
  Changes: Data collection, Database references, Refinement description, Structure summary