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Yorodumi- EMDB-3125: Structural basis for specific recognition of single-stranded RNA ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3125 | |||||||||
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Title | Structural basis for specific recognition of single-stranded RNA by toll-like receptor 13 | |||||||||
Map data | Reconstruction of TLR13 | |||||||||
Sample |
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Function / homology | Function and homology information toll-like receptor 13 signaling pathway / NADP+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / MyD88-dependent toll-like receptor signaling pathway / toll-like receptor signaling pathway / plasma membrane => GO:0005886 / regulation of MAPK cascade / response to virus / transmembrane signaling receptor activity ...toll-like receptor 13 signaling pathway / NADP+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / MyD88-dependent toll-like receptor signaling pathway / toll-like receptor signaling pathway / plasma membrane => GO:0005886 / regulation of MAPK cascade / response to virus / transmembrane signaling receptor activity / signaling receptor activity / rRNA binding / endosome membrane / endosome / inflammatory response / innate immune response / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.87 Å | |||||||||
Authors | Song W / Wang J / Han ZF / Zhang YF / Zhang HQ / Wang WG / Chang JB / Xia BS / Fan SL / Zhang DK ...Song W / Wang J / Han ZF / Zhang YF / Zhang HQ / Wang WG / Chang JB / Xia BS / Fan SL / Zhang DK / Wang JW / Wang HW / Chai JJ | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2015 Title: Structural basis for specific recognition of single-stranded RNA by Toll-like receptor 13. Authors: Wen Song / Jia Wang / Zhifu Han / Yifan Zhang / Heqiao Zhang / Weiguang Wang / Junbiao Chang / Bingshu Xia / Shilong Fan / Dekai Zhang / Jiawei Wang / Hong-Wei Wang / Jijie Chai / Abstract: Toll-like receptors (TLRs) have crucial roles in innate immunity, functioning as pattern-recognition receptors. TLR13 recognizes a conserved sequence from bacterial 23S rRNA and then triggers an ...Toll-like receptors (TLRs) have crucial roles in innate immunity, functioning as pattern-recognition receptors. TLR13 recognizes a conserved sequence from bacterial 23S rRNA and then triggers an immune response. Here we report the crystal structure of the mouse TLR13 ectodomain bound by a 13-nt single-stranded (ss) RNA derived from 23S rRNA. The ssRNA induces TLR13 dimerization but assumes a stem-loop-like structure that is completely different from that in the bacterial ribosome but nevertheless is crucial for TLR13 recognition. Most of the RNA nucleotides are splayed out to make base-specific contacts with the concave surface of TLR13, and RNA-specific interactions are important to allow TLR13 to distinguish RNA from DNA. Interestingly, a viral-derived 16-nt ssRNA predicted to form a similar stem-loop-like structure also induces TLR13 activation. Together, our results reveal the structural mechanism of TLR13's sequence- and conformation-specific recognition of ssRNA. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3125.map.gz | 1.5 MB | EMDB map data format | |
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Header (meta data) | emd-3125-v30.xml emd-3125.xml | 7.3 KB 7.3 KB | Display Display | EMDB header |
Images | EMD-3125.png | 167 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3125 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3125 | HTTPS FTP |
-Validation report
Summary document | emd_3125_validation.pdf.gz | 214.5 KB | Display | EMDB validaton report |
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Full document | emd_3125_full_validation.pdf.gz | 213.6 KB | Display | |
Data in XML | emd_3125_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3125 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3125 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3125.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of TLR13 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : toll-like receptor 13
Entire | Name: toll-like receptor 13 |
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Components |
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-Supramolecule #1000: toll-like receptor 13
Supramolecule | Name: toll-like receptor 13 / type: sample / ID: 1000 / Oligomeric state: One Homotetramer of TLR13 / Number unique components: 1 |
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-Macromolecule #1: TLR13
Macromolecule | Name: TLR13 / type: protein_or_peptide / ID: 1 / Recombinant expression: No |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Oct 3, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.87 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 60788 |