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- EMDB-32844: Toll-like receptor3 linear cluster -

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Basic information

Entry
Database: EMDB / ID: EMD-32844
TitleToll-like receptor3 linear cluster
Map data
Sample
  • Complex: TLR3-poly(I:C) cluster
    • Complex: TLR
      • Protein or peptide: Toll-like receptor 3
    • Complex: poly(I:C)
      • RNA: RNA (80-MER)
      • RNA: RNA (80-MER)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsToll-like receptor / dsRNA / Innate immunity / Receptor / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA complex
Function / homology
Function and homology information


TLR3 deficiency - HSE / response to dsRNA / UNC93B1 deficiency - HSE / type III interferon production / positive regulation of type III interferon production / TICAM1 deficiency - HSE / TRAF3 deficiency - HSE / regulation of dendritic cell cytokine production / Toll Like Receptor 3 (TLR3) Cascade / inflammatory response to wounding ...TLR3 deficiency - HSE / response to dsRNA / UNC93B1 deficiency - HSE / type III interferon production / positive regulation of type III interferon production / TICAM1 deficiency - HSE / TRAF3 deficiency - HSE / regulation of dendritic cell cytokine production / 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 / necroptotic signaling pathway / RIP-mediated NFkB activation via ZBP1 / positive regulation of cytokine production involved in inflammatory response / endolysosome membrane / Trafficking and processing of endosomal TLR / hyperosmotic response / positive regulation of macrophage cytokine production / toll-like receptor signaling pathway / pattern recognition receptor activity / cellular response to exogenous dsRNA / RSV-host interactions / response to exogenous dsRNA / negative regulation of osteoclast differentiation / ubiquitin-like protein ligase binding / positive regulation of interferon-alpha production / cellular response to interferon-beta / positive regulation of chemokine production / JNK cascade / extrinsic apoptotic signaling pathway / positive regulation of interleukin-12 production / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / extracellular matrix / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / positive regulation of interferon-beta production / TICAM1, RIP1-mediated IKK complex recruitment / positive regulation of interleukin-8 production / positive regulation of JNK cascade / microglial cell activation / cellular response to mechanical stimulus / cellular response to virus / cellular response to type II interferon / positive regulation of interleukin-6 production / male gonad development / cellular response to xenobiotic stimulus / 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 / signaling receptor activity / double-stranded RNA binding / defense response to virus / early endosome / positive regulation of canonical NF-kappaB signal transduction / endosome membrane / defense response to bacterium / positive regulation of apoptotic process / Golgi membrane / lysosomal membrane / innate immune response / positive regulation of gene expression / endoplasmic reticulum membrane / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / membrane / 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
Toll-like receptor 3
Similarity search - Component
Biological speciesHuman (human) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.26 Å
AuthorsLim CS / Jang YH / Lee GY / Han GM / Lee JO
Funding support Korea, Republic Of, 2 items
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, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32844.png

Downloads & links

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Map

FileDownload / File: emd_32844.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 480 pix.
= 397.512 Å		0.83 Å/pix.
x 480 pix.
= 397.512 Å		0.83 Å/pix.
x 480 pix.
= 397.512 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82815 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-27.196580000000001 - 50.435769999999998
Average (Standard dev.)-0.017770039 (±0.9851933)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 397.512 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : TLR3-poly(I:C) cluster

EntireName: TLR3-poly(I:C) cluster
Components
  • Complex: TLR3-poly(I:C) cluster
    • Complex: TLR
      • Protein or peptide: Toll-like receptor 3
    • Complex: poly(I:C)
      • RNA: RNA (80-MER)
      • RNA: RNA (80-MER)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: TLR3-poly(I:C) cluster

SupramoleculeName: TLR3-poly(I:C) cluster / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: TLR

SupramoleculeName: TLR / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human (human)

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Supramolecule #3: poly(I:C)

SupramoleculeName: poly(I:C) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3

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Macromolecule #1: Toll-like receptor 3

MacromoleculeName: Toll-like receptor 3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 102.376281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: STTKCTVSHE VADCSHLKLT QVPDDLPTNI TVLNLTHNQL RRLPAANFTR YSQLTSLDVG FNTISKLEPE LCQKLPMLKV LNLQHNELS QLSDKTFAFC TNLTELHLMS NSIQKIKNNP FVKQKNLITL DLSHNGLSST KLGTQVQLEN LQELLLSNNK I QALKSEEL ...String:
STTKCTVSHE VADCSHLKLT QVPDDLPTNI TVLNLTHNQL RRLPAANFTR YSQLTSLDVG FNTISKLEPE LCQKLPMLKV LNLQHNELS QLSDKTFAFC TNLTELHLMS NSIQKIKNNP FVKQKNLITL DLSHNGLSST KLGTQVQLEN LQELLLSNNK I QALKSEEL DIFANSSLKK LELSSNQIKE FSPGCFHAIG RLFGLFLNNV QLGPSLTEKL CLELANTSIR NLSLSNSQLS TT SNTTFLG LKWTNLTMLD LSYNNLNVVG NDSFAWLPQL EYFFLEYNNI QHLFSHSLHG LFNVRYLNLK RSFTKQSISL ASL PKIDDF SFQWLKCLEH LNMEDNDIPG IKSNMFTGLI NLKYLSLSNS FTSLRTLTNE TFVSLAHSPL HILNLTKNKI SKIE SDAFS WLGHLEVLDL GLNEIGQELT GQEWRGLENI FEIYLSYNKY LQLTRNSFAL VPSLQRLMLR RVALKNVDSS PSPFQ PLRN LTILDLSNNN IANINDDMLE GLEKLEILDL QHNNLARLWK HANPGGPIYF LKGLSHLHIL NLESNGFDEI PVEVFK DLF ELKIIDLGLN NLNTLPASVF NNQVSLKSLN LQKNLITSVE KKVFGPAFRN LTELDMRFNP FDCTCESIAW FVNWINE TH TNIPELSSHY LCNTPPHYHG FPVRLFDTSS CKDSAPFELF FMINTSILLI FIFIVLLIHF EGWRISFYWN VSVHRVLG F KEIDRQTEQF EYAAYIIHAY KDKDWVWEHF SSMEKEDQSL KFCLEERDFE AGVFELEAIV NSIKRSRKII FVITHHLLK DPLCKRFKVH HAVQQAIEQN LDSIILVFLE EIPDYKLNHA LCLRRGMFKS HCILNWPVQK ERIGAFRHKL QVALGSKNSV HSNSLEVLF Q

UniProtKB: Toll-like receptor 3

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Macromolecule #2: RNA (80-MER)

MacromoleculeName: RNA (80-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 24.369598 KDa
SequenceString:
CCCCCCCCCC CCCCCCCCCC CCCCCCCCCC CCCCCCCCCC CCCCCCCCCC CCCCCCCCCC CCCCCCCCCC CCCCCCCCCC

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Macromolecule #3: RNA (80-MER)

MacromoleculeName: RNA (80-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 26.370277 KDa
SequenceString:
IIIIIIIIII IIIIIIIIII IIIIIIIIII IIIIIIIIII IIIIIIIIII IIIIIIIIII IIIIIIIIII IIIIIIIIII

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 28 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration7.2 mg/mL
BufferpH: 5.5
Component:
ConcentrationFormulaName
20.0 mMC6H13NO4S2-(N-morpholino)ethanesulfonic acid
150.0 mMNaClsodium chloride
0.03 %C19H42NO4Pn-Tetradecylphosphocholine
GridModel: 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. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 982514
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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Atomic model buiding 1

Initial modelPDB ID:

3ulu


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-7wv3:
Toll-like receptor3 linear cluster

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