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- EMDB-3125: Structural basis for specific recognition of single-stranded RNA ... -

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Basic information

Entry
Database: EMDB / ID: EMD-3125
TitleStructural basis for specific recognition of single-stranded RNA by toll-like receptor 13
Map dataReconstruction of TLR13
Sample
  • Sample: toll-like receptor 13
  • Protein or peptide: TLR13
Function / homology
Function and homology information


toll-like receptor 13 signaling pathway / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / 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 / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / 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 / endosome membrane / rRNA binding / endosome / inflammatory response / innate immune response / identical protein binding / cytoplasm
Similarity search - Function
Toll-like receptor / TIR domain / Leucine Rich Repeat / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...Toll-like receptor / TIR domain / Leucine Rich Repeat / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Toll-like receptor 13
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.87 Å
AuthorsSong 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
CitationJournal: 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
DepositionAug 13, 2015-
Header (metadata) releaseAug 19, 2015-
Map releaseSep 23, 2015-
UpdateOct 21, 2015-
Current statusOct 21, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3125.png

Downloads & links

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Map

FileDownload / File: emd_3125.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of TLR13
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy EMDB: 0.05 / Movie #1: 0.04
Minimum - Maximum-0.08338065 - 0.15362608
Average (Standard dev.)0.00133443 (±0.0084467)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 190.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z190.080190.080190.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS144144144
D min/max/mean-0.0830.1540.001

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Supplemental data

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Sample components

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Entire : toll-like receptor 13

EntireName: toll-like receptor 13
Components
  • Sample: toll-like receptor 13
  • Protein or peptide: TLR13

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Supramolecule #1000: toll-like receptor 13

SupramoleculeName: 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

MacromoleculeName: TLR13 / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Mus musculus (house mouse)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateOct 3, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k)
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied 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

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