5ZSI | pdb_00005zsi

Crystal structure of monkey TLR7 in complex with CL097


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.259 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Structural Analyses of Toll-like Receptor 7 Reveal Detailed RNA Sequence Specificity and Recognition Mechanism of Agonistic Ligands.

Zhang, Z.Ohto, U.Shibata, T.Taoka, M.Yamauchi, Y.Sato, R.Shukla, N.M.David, S.A.Isobe, T.Miyake, K.Shimizu, T.

(2018) Cell Rep 25: 3371-3381.e5

  • DOI: https://doi.org/10.1016/j.celrep.2018.11.081
  • Primary Citation Related Structures: 
    5ZSA, 5ZSB, 5ZSC, 5ZSD, 5ZSE, 5ZSF, 5ZSG, 5ZSH, 5ZSI, 5ZSJ, 5ZSL, 5ZSM, 5ZSN, 6IF5

  • PubMed Abstract: 

    Toll-like receptor 7 (TLR7) is an innate immune receptor for single-stranded RNA (ssRNA) and has important roles in infectious diseases. We previously reported that TLR7 shows synergistic activation in response to two ligands, guanosine and ssRNA. However, the specific ssRNA sequence preference, detailed recognition mode of TLR7 and its ligand, and molecular determinants of TLR7 and TLR8 selectivity remain unknown. Here, we report on TLR7 from a large-scale crystallographic study combined with a multifaceted approach. We reveal that successive uridine-containing ssRNAs fully or moderately bind TLR7, whereas single uridine-containing ssRNAs have reduced affinities. We also reveal the detailed relationships between the chemical structures of ligands and their binding to TLR7. We demonstrate that an engineered TLR8 mutant alters its responsiveness to TLR7-specific ligands. Finally, we identify guanosine 2',3'-cyclic phosphate (2',3'-cGMP) as a possible endogenous ligand for TLR7 with greater affinity than guanosine. The abundant structural information will facilitate future development of treatments targeting TLR7.


  • Organizational Affiliation
    • Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Macromolecule Content 

  • Total Structure Weight: 193.31 kDa 
  • Atom Count: 12,927 
  • Modeled Residue Count: 1,544 
  • Deposited Residue Count: 1,646 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Toll-like receptor 7A [auth B],
B [auth A]
823Macaca mulattaMutation(s): 4 
Gene Names: TLR7
UniProt
Find proteins for B3Y653 (Macaca mulatta)
Explore B3Y653 
Go to UniProtKB:  B3Y653
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3Y653
Glycosylation
Glycosylation Sites: 6
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C09
(Subject of Investigation/LOI)

Query on C09



Download:Ideal Coordinates CCD File
J [auth B],
R [auth A]
2-(ethoxymethyl)-1H-imidazo[4,5-c]quinolin-4-amine
C13 H14 N4 O
DEVCLHVFELRPIU-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth B]
E [auth B]
F [auth B]
G [auth B]
H [auth B]
D [auth B],
E [auth B],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
K [auth B],
L [auth B],
S [auth A],
T [auth A],
U [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.259 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.366α = 90
b = 139.951β = 90
c = 149.468γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-03-13
    Changes: Data collection, Database references, Structure summary
  • Version 2.2: 2024-10-30
    Changes: Structure summary