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- PDB-7wv4: ectoTLR3-poly(I:C) cluster -

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Basic information

Entry
Database: PDB / ID: 7wv4
TitleectoTLR3-poly(I:C) cluster
Components
  • (RNA (80-MER)) x 2
  • Toll-like receptor 3
KeywordsIMMUNE SYSTEM/RNA / Toll-like receptor / dsRNA / Innate immunity / Receptor / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA complex
Function / homology
Function and homology information


TLR3 deficiency - HSE / UNC93B1 deficiency - HSE / TICAM1 deficiency - HSE / response to dsRNA / TRAF3 deficiency - HSE / Toll Like Receptor 3 (TLR3) Cascade / inflammatory response to wounding / TLR3-mediated TICAM1-dependent programmed cell death / activation of NF-kappaB-inducing kinase activity / toll-like receptor 3 signaling pathway ...TLR3 deficiency - HSE / UNC93B1 deficiency - HSE / TICAM1 deficiency - HSE / response to dsRNA / TRAF3 deficiency - HSE / Toll Like Receptor 3 (TLR3) Cascade / inflammatory response to wounding / TLR3-mediated TICAM1-dependent programmed cell death / activation of NF-kappaB-inducing kinase activity / toll-like receptor 3 signaling pathway / detection of virus / hyperosmotic response / negative regulation of osteoclast differentiation / necroptotic signaling pathway / RIP-mediated NFkB activation via ZBP1 / Trafficking and processing of endosomal TLR / endolysosome membrane / positive regulation of cytokine production involved in inflammatory response / toll-like receptor signaling pathway / response to exogenous dsRNA / pattern recognition receptor activity / RSV-host interactions / positive regulation of interferon-alpha production / ubiquitin-like protein ligase binding / JNK cascade / extrinsic apoptotic signaling pathway / positive regulation of interleukin-12 production / positive regulation of chemokine production / positive regulation of interferon-beta production / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / positive regulation of interleukin-8 production / TICAM1, RIP1-mediated IKK complex recruitment / cellular response to mechanical stimulus / cellular response to virus / positive regulation of interleukin-6 production / positive regulation of JNK cascade / positive regulation of type II interferon production / positive regulation of angiogenesis / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / double-stranded RNA binding / signaling receptor activity / defense response to virus / early endosome / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / endosome membrane / Golgi membrane / innate immune response / lysosomal membrane / positive regulation of gene expression / endoplasmic reticulum membrane / signal transduction / positive regulation of transcription by RNA polymerase II / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Toll-like receptor 3 trans-membrane domain / Toll-like receptor 3 trans-membrane domain / TIR domain / Leucine Rich repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / Leucine-rich repeat, SDS22-like subfamily / Toll/interleukin-1 receptor homology (TIR) domain ...Toll-like receptor 3 trans-membrane domain / Toll-like receptor 3 trans-membrane domain / TIR domain / Leucine Rich repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / 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) / Toll-like receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsLim, C.S. / Jang, Y.H. / Lee, G.Y. / Han, G.M. / Lee, J.O.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019M3E5D6066058 Korea, Republic Of
National Research Foundation (NRF, Korea)2017M3A9F6029753 Korea, Republic Of
CitationJournal: 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
DepositionFeb 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Refinement description
Category: citation / citation_author / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 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_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

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toll-like receptor 3
B: Toll-like receptor 3
C: Toll-like receptor 3
D: Toll-like receptor 3
E: RNA (80-MER)
F: RNA (80-MER)


Theoretical massNumber of molelcules
Total (without water)364,4336
Polymers364,4336
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Toll-like receptor 3


Mass: 78423.375 Da / Num. of mol.: 4 / Fragment: ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR3 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O15455
#2: RNA chain RNA (80-MER)


Mass: 24369.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (80-MER)


Mass: 26370.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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

Component
IDNameTypeEntity IDParent-IDSource
1ectoTLR3-poly(I:C) clusterCOMPLEXall0MULTIPLE SOURCES
2Toll-like receptor 3COMPLEX#11RECOMBINANT
3poly(I:C)COMPLEX#2-#31SYNTHETIC
Molecular weightExperimental value: NO
Source (natural)Organism: Human (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 5.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM2-(N-morpholino)ethanesulfonic acidC6H13NO4S1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 1.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
7UCSF ChimeraXmodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59774 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13ULU

3ulu

13ULU1PDBexperimental model
23CIY

3ciy

13CIY2PDBexperimental model

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