+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34361 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | TLR3(A795H)-poly(I:C) complex | |||||||||
Map data | TLR3(A795H)-poly(I:C) complex | |||||||||
Sample |
| |||||||||
Biological species | Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.47 Å | |||||||||
Authors | Lim CS / Jang YH / Lee GY / Han GM / Lee JO | |||||||||
Funding support | Korea, Republic Of, 2 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2022 Title: TLR3 forms a highly organized cluster when bound to a poly(I:C) RNA ligand. Authors: Chan Seok Lim / Yoon Ha Jang / Ga Young Lee / Gu Min Han / Hye Jin Jeong / Ji Won Kim / Jie-Oh Lee / Abstract: Toll-like Receptor 3 (TLR3) initiates a potent anti-viral immune response by binding to double-stranded RNA ligands. Previous crystallographic studies showed that TLR3 forms a homodimer when bound to ...Toll-like Receptor 3 (TLR3) initiates a potent anti-viral immune response by binding to double-stranded RNA ligands. Previous crystallographic studies showed that TLR3 forms a homodimer when bound to a 46-base pair RNA ligand. However, this short RNA fails to initiate a robust immune response. To obtain structural insights into the length dependency of TLR3 ligands, we determine the cryo-electron microscopy structure of full-length TLR3 in a complex with a synthetic RNA ligand with an average length of ~400 base pairs. In the structure, the dimeric TLR3 units are clustered along the double-stranded RNA helix in a highly organized and cooperative fashion with a uniform inter-dimer spacing of 103 angstroms. The intracellular and transmembrane domains are dispensable for the clustering because their deletion does not interfere with the cluster formation. Our structural observation suggests that ligand-induced clustering of TLR3 dimers triggers the ordered assembly of intracellular signaling adaptors and initiates a robust innate immune response. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_34361.map.gz | 49.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-34361-v30.xml emd-34361.xml | 15.6 KB 15.6 KB | Display Display | EMDB header |
Images | emd_34361.png | 42 KB | ||
Others | emd_34361_half_map_1.map.gz emd_34361_half_map_2.map.gz | 49 MB 49 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34361 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34361 | HTTPS FTP |
-Validation report
Summary document | emd_34361_validation.pdf.gz | 900.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_34361_full_validation.pdf.gz | 900 KB | Display | |
Data in XML | emd_34361_validation.xml.gz | 12 KB | Display | |
Data in CIF | emd_34361_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34361 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34361 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_34361.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | TLR3(A795H)-poly(I:C) complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.702 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: TLR3(A795H)-poly(I:C) complex halfmapB
File | emd_34361_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | TLR3(A795H)-poly(I:C) complex halfmapB | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: TLR3(A795H)-poly(I:C) complex halfmapA
File | emd_34361_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | TLR3(A795H)-poly(I:C) complex halfmapA | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : TLR3(A795H)-poly(I:C) cluster
Entire | Name: TLR3(A795H)-poly(I:C) cluster |
---|---|
Components |
|
-Supramolecule #1: TLR3(A795H)-poly(I:C) cluster
Supramolecule | Name: TLR3(A795H)-poly(I:C) cluster / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
---|
-Supramolecule #2: TLR(A795H)
Supramolecule | Name: TLR(A795H) / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Human (human) |
-Supramolecule #3: poly(I:C)
Supramolecule | Name: poly(I:C) / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
---|
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.56 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 5.5 Component:
| ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 37215 |
---|---|
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
---|