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- EMDB-30624: Mouse Toll-like receptor 3 ectodomain in complex with lncRNA Rmrp... -

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Basic information

Entry
Database: EMDB / ID: EMD-30624
TitleMouse Toll-like receptor 3 ectodomain in complex with lncRNA Rmrp in elongated form
Map data
Sample
  • Complex: Cryo-EM structure of mouse Toll-like receptor 3 ectodomain with C-domain of lncRNA Rmrp
    • Protein or peptide: Toll-like receptor 3
    • RNA: RNA component of mitochondrial RNAase P (Rmrp), RNase MRP RNA
Keywordscomplex / 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 / 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 / toll-like receptor signaling pathway / pattern recognition receptor activity ...type III interferon production / positive regulation of type III interferon production / 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 / toll-like receptor signaling pathway / pattern recognition receptor activity / cellular response to exogenous dsRNA / response to exogenous dsRNA / ubiquitin-like protein ligase binding / 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 / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / defense response / cellular response to virus / cellular response to type II interferon / positive regulation of interleukin-6 production / response to virus / male gonad development / cellular response to xenobiotic stimulus / positive regulation of type II interferon production / positive regulation of angiogenesis / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / MAPK cascade / double-stranded RNA binding / defense response to virus / early endosome / endosome membrane / positive regulation of canonical NF-kappaB signal transduction / 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 / 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 speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsLi B / Cao X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81788101 China
CitationJournal: Cell Res / Year: 2025
Title: Molecular characterization of endosomal self RNA Rmrp-engaged TLR3 dimerization to prime innate activation.
Authors: Shikun Zhang / Bo Li / Lun Liu / Dongsheng Gong / Deyu Zhang / Fengjiang Liu / Xiuna Yang / Hua Qin / Deling Kong / Shuyang Zhang / Zihe Rao / Xuetao Cao /
Abstract: The pre-dimerization of endosome-localized RNA sensor Toll-like receptor 3 (TLR3) is required for its innate recognition, yet how TLR3 pre-dimers are formed and precisely primed for innate activation ...The pre-dimerization of endosome-localized RNA sensor Toll-like receptor 3 (TLR3) is required for its innate recognition, yet how TLR3 pre-dimers are formed and precisely primed for innate activation remains unclear. Here, we demonstrate that endosome-localized self RNA Rmrp directly binds to TLR3 and induces TLR3 dimerization in the early endosome but does not interact with endosome-localized TLR7, TLR8, TLR9 or cytoplasmic RNA sensor RIG-I under homeostatic conditions. Cryo-EM structure of Rmrp-TLR3 complex reveals a novel lapped conformation of TLR3 dimer engaged by Rmrp, which is distinct from the activation mechanism by dsRNA and the specific structural feature at the 3'-end of Rmrp is critical for its functional interaction with TLR3. Furthermore, K42 residue of TLR3 is essential for binding to Rmrp and subsequent dimerization. Rmrp dissociates from TLR3 following endosomal acidification, generating a matured TLR3 dimer which is primed for innate recognition and activation. Myeloid-cell deficiency of Rmrp reduces TLR3 dimerization and attenuates TLR3-mediated antiviral responses against influenza A both in vitro and in vivo. These findings elucidate the structural mode of self RNA Rmrp-primed TLR3 dimerization and ready for efficient innate recognition on endosomal membrane, extending our knowledge of how membrane-associated TLRs pre-dimerize and suggesting a new function of subcellular localized self RNAs in empowering innate activation.
History
DepositionOct 15, 2020-
Header (metadata) releaseOct 20, 2021-
Map releaseOct 20, 2021-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7da7
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30624.png

Downloads & links

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Map

FileDownload / File: emd_30624.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.3
Minimum - Maximum-0.80397487 - 1.6417792
Average (Standard dev.)0.0026856775 (±0.04095878)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z314.880314.880314.880
α/β/γ90.00090.00090.000
start NX/NY/NZ-250-250-250
NX/NY/NZ500500500
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.8041.6420.003

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of mouse Toll-like receptor 3 ectodomain with C...

EntireName: Cryo-EM structure of mouse Toll-like receptor 3 ectodomain with C-domain of lncRNA Rmrp
Components
  • Complex: Cryo-EM structure of mouse Toll-like receptor 3 ectodomain with C-domain of lncRNA Rmrp
    • Protein or peptide: Toll-like receptor 3
    • RNA: RNA component of mitochondrial RNAase P (Rmrp), RNase MRP RNA

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Supramolecule #1: Cryo-EM structure of mouse Toll-like receptor 3 ectodomain with C...

SupramoleculeName: Cryo-EM structure of mouse Toll-like receptor 3 ectodomain with C-domain of lncRNA Rmrp
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 230 KDa

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Macromolecule #1: Toll-like receptor 3

MacromoleculeName: Toll-like receptor 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 78.101648 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: HHHHHHENLY FQSQCTVRYN VADCSHLKLT HIPDDLPSNI TVLNLTHNQL RRLPPTNFTR YSQLAILDAG FNSISKLEPE LCQILPLLK VLNLQHNELS QISDQTFVFC TNLTELDLMS NSIHKIKSNP FKNQKNLIKL DLSHNGLSST KLGTGVQLEN L QELLLAKN ...String:
HHHHHHENLY FQSQCTVRYN VADCSHLKLT HIPDDLPSNI TVLNLTHNQL RRLPPTNFTR YSQLAILDAG FNSISKLEPE LCQILPLLK VLNLQHNELS QISDQTFVFC TNLTELDLMS NSIHKIKSNP FKNQKNLIKL DLSHNGLSST KLGTGVQLEN L QELLLAKN KILALRSEEL EFLGNSSLRK LDLSSNPLKE FSPGCFQTIG KLFALLLNNA QLNPHLTEKL CWELSNTSIQ NL SLANNQL LATSESTFSG LKWTNLTQLD LSYNNLHDVG NGSFSYLPSL RYLSLEYNNI QRLSPRSFYG LSNLRYLSLK RAF TKQSVS LASHPNIDDF SFQWLKYLEY LNMDDNNIPS TKSNTFTGLV SLKYLSLSKT FTSLQTLTNE TFVSLAHSPL LTLN LTKNH ISKIANGTFS WLGQLRILDL GLNEIEQKLS GQEWRGLRNI FEIYLSYNKY LQLSTSSFAL VPSLQRLMLR RVALK NVDI SPSPFRPLRN LTILDLSNNN IANINEDLLE GLENLEILDF QHNNLARLWK RANPGGPVNF LKGLSHLHIL NLESNG LDE IPVGVFKNLF ELKSINLGLN NLNKLEPFIF DDQTSLRSLN LQKNLITSVE KDVFGPPFQN LNSLDMRFNP FDCTCES IS WFVNWINQTH TNISELSTHY LCNTPHHYYG FPLKLFDTSS CK

UniProtKB: Toll-like receptor 3

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Macromolecule #2: RNA component of mitochondrial RNAase P (Rmrp), RNase MRP RNA

MacromoleculeName: RNA component of mitochondrial RNAase P (Rmrp), RNase MRP RNA
type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 48.12452 KDa
SequenceString:
GCUCGCUCUG AAGGCCUGUU UCCUAGGCUA CAUACGAGGG ACAUGUUCCU UAUCCUUUCG CCUAGGGGAA AGUCCCCGGA AGCUCACAU AGUGACGCAG GCAGUGCGAC CUGGCUCGCA CCAACCACAC GGGGCUCAUU CUCAGCGCGG C

GENBANK: GENBANK: NR_001460.1, GENBANK: NR_001460.1

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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

Concentration1.0 mg/mL
BufferpH: 6
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was mono disperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 78.5 K / Max: 78.5 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 40 eV
DetailsPreliminary grid screening was preformed manually.
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Number grids imaged: 2 / Number real images: 10617 / Average exposure time: 5.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe selected images were normalized.
Particle selectionNumber selected: 2545278
CTF correctionSoftware - Name: cryoSPARC (ver. 2.9.1) / Details: CTF correction was done by patch CTF correction. / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: The startup models were generated automatically.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.9.1) / Number images used: 108128
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.9.1)
Details: The initial angle assignment was generated by Ab-initio reconstruction.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.9.1)
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. 2.9.1)

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Atomic model buiding 1

Initial modelPDB ID:

3cig


Chain - Chain ID: A / Chain - Residue range: 27-697 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT / Overall B value: 97.5 / Target criteria: correlation coefficient
Output model

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

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