+Open data
-Basic information
Entry | Database: PDB / ID: 7ytp | ||||||
---|---|---|---|---|---|---|---|
Title | TLR7 in complex with an inhibitor | ||||||
Components | Toll-like receptor 7 | ||||||
Keywords | IMMUNE SYSTEM / TLR7 / antagonist | ||||||
Function / homology | Function and homology information toll-like receptor 7 signaling pathway / response to cGMP / siRNA binding / early phagosome / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / canonical NF-kappaB signal transduction / positive regulation of interferon-alpha production / positive regulation of chemokine production ...toll-like receptor 7 signaling pathway / response to cGMP / siRNA binding / early phagosome / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / canonical NF-kappaB signal transduction / positive regulation of interferon-alpha production / positive regulation of chemokine production / JNK cascade / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / regulation of protein phosphorylation / cellular response to virus / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / positive regulation of interleukin-6 production / double-stranded RNA binding / positive regulation of type II interferon production / defense response to virus / single-stranded RNA binding / lysosome / receptor complex / endosome / inflammatory response / innate immune response / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Macaca mulatta (Rhesus monkey) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å | ||||||
Authors | Zhang, Z. / Ohto, U. / Shimizu, T. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: To Be Published Title: TLR7 in complex with an inhibitor Authors: Zhang, Z. / Shimizu, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ytp.cif.gz | 284.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ytp.ent.gz | 223.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ytp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ytp_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7ytp_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7ytp_validation.xml.gz | 50.3 KB | Display | |
Data in CIF | 7ytp_validation.cif.gz | 75.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/7ytp ftp://data.pdbj.org/pub/pdb/validation_reports/yt/7ytp | HTTPS FTP |
-Related structure data
Related structure data | 34091MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 111561.273 Da / Num. of mol.: 2 / Fragment: extracellular domain,extracellular domain Mutation: N145Q/N367Q/S418L/E419V/V420P/G421R/F422G/C423S/N466Q/N777Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: TLR7 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: B3Y653 #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: Chemical | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: TLR7 in complex with an inhibitor / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.2 MDa / Experimental value: NO |
Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Source (recombinant) | Organism: Drosophila melanogaster (fruit fly) |
Buffer solution | pH: 4.8 |
Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 61.1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software | Name: RELION / Version: 3.1.1 / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91789 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|