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- EMDB-34361: TLR3(A795H)-poly(I:C) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-34361
TitleTLR3(A795H)-poly(I:C) complex
Map dataTLR3(A795H)-poly(I:C) complex
Sample
  • Complex: TLR3(A795H)-poly(I:C) cluster
    • Complex: TLR(A795H)
    • Complex: poly(I:C)
Biological speciesHuman (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.47 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
DepositionSep 21, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateDec 7, 2022-
Current statusDec 7, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34361.png

Downloads & links

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Map

FileDownload / File: emd_34361.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTLR3(A795H)-poly(I:C) complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 240 pix.
= 408.48 Å		1.7 Å/pix.
x 240 pix.
= 408.48 Å		1.7 Å/pix.
x 240 pix.
= 408.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.702 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.17294037 - 0.71439123
Average (Standard dev.)0.0013231193 (±0.028585788)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 408.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: TLR3(A795H)-poly(I:C) complex halfmapB

Fileemd_34361_half_map_1.map
AnnotationTLR3(A795H)-poly(I:C) complex halfmapB
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: TLR3(A795H)-poly(I:C) complex halfmapA

Fileemd_34361_half_map_2.map
AnnotationTLR3(A795H)-poly(I:C) complex halfmapA
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TLR3(A795H)-poly(I:C) cluster

EntireName: TLR3(A795H)-poly(I:C) cluster
Components
  • Complex: TLR3(A795H)-poly(I:C) cluster
    • Complex: TLR(A795H)
    • Complex: poly(I:C)

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Supramolecule #1: TLR3(A795H)-poly(I:C) cluster

SupramoleculeName: TLR3(A795H)-poly(I:C) cluster / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: TLR(A795H)

SupramoleculeName: TLR(A795H) / type: complex / Chimera: Yes / 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 / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2-#3

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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

Concentration0.56 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.
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: 2.4 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 37215
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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