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- PDB-7da7: Mouse Toll-like receptor 3 ectodomain in complex with lncRNA Rmrp... -

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Basic information

Entry
Database: PDB / ID: 7da7
TitleMouse Toll-like receptor 3 ectodomain in complex with lncRNA Rmrp in elongated form
Components
  • RNA component of mitochondrial RNAase P (Rmrp), RNase MRP RNA
  • Toll-like receptor 3
KeywordsRNA BINDING PROTEIN/RNA / complex / innate immune system / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


type III interferon production / positive regulation of type III interferon production / response to dsRNA / regulation of dendritic cell cytokine production / inflammatory response to wounding / toll-like receptor 3 signaling pathway / necroptotic signaling pathway / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage cytokine production / pattern recognition receptor activity ...type III interferon production / positive regulation of type III interferon production / response to dsRNA / regulation of dendritic cell cytokine production / inflammatory response to wounding / toll-like receptor 3 signaling pathway / necroptotic signaling pathway / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / cellular response to exogenous dsRNA / response to exogenous dsRNA / positive regulation of interferon-alpha production / positive regulation of type I interferon production / cellular response to interferon-beta / positive regulation of chemokine production / JNK cascade / extrinsic apoptotic signaling pathway / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / microglial cell activation / response to virus / cellular response to virus / cellular response to type II interferon / defense response / positive regulation of interleukin-6 production / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / positive regulation of angiogenesis / male gonad development / positive regulation of tumor necrosis factor production / MAPK cascade / transmembrane signaling receptor activity / double-stranded RNA binding / cellular response to xenobiotic stimulus / signaling receptor activity / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / early endosome / endosome membrane / inflammatory response / positive regulation of apoptotic process / innate immune response / endoplasmic reticulum membrane / cell surface / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane
Similarity search - Function
Toll-like receptor 3 trans-membrane domain / Toll-like receptor 3 trans-membrane domain / Toll-like receptor / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine Rich Repeat / Toll - interleukin 1 - resistance / TIR domain profile. / Leucine-rich repeat, SDS22-like subfamily ...Toll-like receptor 3 trans-membrane domain / Toll-like receptor 3 trans-membrane domain / Toll-like receptor / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine Rich Repeat / Toll - interleukin 1 - resistance / TIR domain profile. / Leucine-rich repeat, SDS22-like subfamily / 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
: / RNA / RNA (> 10) / RNA (> 100) / Toll-like receptor 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsLi, B. / Cao, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81788101 China
CitationJournal: To Be Published
Title: Endosomal lncRNA Rmrp is required for TLR3 innate sensing by engaging TLR3 dimerization
Authors: Zhang, S. / Li, B. / Cao, X.
History
DepositionOct 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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  • Deposited structure unit
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  • EMDB-30624
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Toll-like receptor 3
B: Toll-like receptor 3
C: RNA component of mitochondrial RNAase P (Rmrp), RNase MRP RNA


Theoretical massNumber of molelcules
Total (without water)204,3283
Polymers204,3283
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Toll-like receptor 3


Mass: 78101.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tlr3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q99MB1
#2: RNA chain RNA component of mitochondrial RNAase P (Rmrp), RNase MRP RNA / lncRNA Rmrp


Mass: 48124.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: GenBank: NR_001460
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of mouse Toll-like receptor 3 ectodomain with C-domain of lncRNA Rmrp
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.23 MDa / Experimental value: YES
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 6
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was mono disperse.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: Preliminary grid screening was preformed manually.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 78.5 K / Temperature (min): 78.5 K
Image recordingAverage exposure time: 5 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 10617
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 40 eV
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4cryoSPARC2.9.1CTF correction
7UCSF Chimera1.14model fitting
9cryoSPARC2.9.1initial Euler assignment
10cryoSPARC2.9.1final Euler assignment
11cryoSPARC2.9.1classification
12cryoSPARC2.9.13D reconstruction
13PHENIX1.16model refinement
Image processingDetails: The selected images were normalized.
CTF correctionDetails: CTF correction was done by patch CTF correction. / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2545278
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108128 / Symmetry type: POINT
Atomic model buildingB value: 97.5 / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Atomic model buildingPDB-ID: 3CIG

3cig


Pdb chain-ID: A / Accession code: 3CIG / Pdb chain residue range: 27-697 / Source name: PDB / Type: experimental model

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