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- EMDB-63406: Cryo-EM analysis of TLR7 in complex with mGrUrC -

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Basic information

Entry
Database: EMDB / ID: EMD-63406
TitleCryo-EM analysis of TLR7 in complex with mGrUrC
Map data
Sample
  • Complex: TLR7 in complex with mGrUrC
    • Protein or peptide: Toll-like receptor 7
    • RNA: RNA (5'-R(*(OMG)P*UP*C)-3')
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsTLR7 / Toll like receptor / RNA / IMMUNE SYSTEM
Function / homology
Function and homology information


toll-like receptor 7 signaling pathway / toll-like receptor 8 signaling pathway / response to cGMP / siRNA binding / early phagosome / endolysosome membrane / toll-like receptor signaling pathway / positive regulation of macrophage cytokine production / pattern recognition receptor activity / positive regulation of interferon-alpha production ...toll-like receptor 7 signaling pathway / toll-like receptor 8 signaling pathway / response to cGMP / siRNA binding / early phagosome / endolysosome membrane / toll-like receptor signaling pathway / positive regulation of macrophage cytokine production / pattern recognition receptor activity / positive regulation of interferon-alpha production / canonical NF-kappaB signal transduction / positive regulation of chemokine production / JNK cascade / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / cellular response to mechanical stimulus / cellular response to virus / positive regulation of interleukin-6 production / positive regulation of type II interferon production / positive regulation of inflammatory response / double-stranded RNA binding / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / receptor complex / single-stranded RNA binding / inflammatory response / innate immune response / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / metal ion binding / plasma membrane
Similarity search - Function
TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Leucine-rich repeat, SDS22-like subfamily / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype ...TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Leucine-rich repeat, SDS22-like subfamily / 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 7
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhang Z / Ohto U / Shimizu T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM analysis of TLR7 in complex with mGrUrC
Authors: Gantier M
History
DepositionFeb 10, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63406.png

Downloads & links

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Map

FileDownload / File: emd_63406.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.028
Minimum - Maximum-0.06911224 - 0.17702867
Average (Standard dev.)-0.000051169 (±0.005312505)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_63406_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63406_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63406_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : TLR7 in complex with mGrUrC

EntireName: TLR7 in complex with mGrUrC
Components
  • Complex: TLR7 in complex with mGrUrC
    • Protein or peptide: Toll-like receptor 7
    • RNA: RNA (5'-R(*(OMG)P*UP*C)-3')
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: TLR7 in complex with mGrUrC

SupramoleculeName: TLR7 in complex with mGrUrC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Macromolecule #1: Toll-like receptor 7

MacromoleculeName: Toll-like receptor 7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 94.745594 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: RSPWARWFPK TLPCDVTLDV SKNHVIVDCT DKHLTEIPGG IPTNTTNLTL TINHIPDISP ASFHRLVHLV EIDFRCNCVP IRLGSKSNM CPRRLQIKPR SFSGLTYLKS LYLDGNQLLE IPQGLPPSLQ LLSLEANNIF SIRKEQLTEL ANIEILYLGQ N CYYRNPCY ...String:
RSPWARWFPK TLPCDVTLDV SKNHVIVDCT DKHLTEIPGG IPTNTTNLTL TINHIPDISP ASFHRLVHLV EIDFRCNCVP IRLGSKSNM CPRRLQIKPR SFSGLTYLKS LYLDGNQLLE IPQGLPPSLQ LLSLEANNIF SIRKEQLTEL ANIEILYLGQ N CYYRNPCY VSYSIEKDAF LNLTKLKVLS LKDNNVTTVP TVLPSTLTEL YLYNNMIAEI QEDDFNNLNQ LQILDLSGNC PR CYNAPFP CTPCKNNSPL QIPVNAFDAL TELKVLRLHS NSLQHVPPRW FKNINNLQEL DLSQNFLAKE IGDAKFLHFL PNL IQLDLS FNFELQVYRA SMNLSQAFSS LKSLKILRIR GYVFKELKSF QLSPLHNLQN LEVLDLGTNF IKIANLSMFK QFKR LKVID LSVNKISPSG DSLVPRGSSN ARTSVESYEP QVLEQLYYFR YDKYARSCRF KNKEASFTSV QESCYKYGQT LDLSK NSIF FIKSSDFQHL SFLKCLNLSG NLISQTLNGS EFQPLAELRY LDFSNNRLDL LHSTAFEELR KLEVLDISSN SHYFQS EGI THMLNFTKNL KVLQKLMMND NDISSSTSRT MESESLRTLE FRGNHLDVLW RDGDNRYLQL FKNLLKLEEL DISKNSL SF LPSGVFDGMP PNLKNLSLAK NGLKSFIWEK LRYLKNLETL DLSHNQLTTV PERLSNCSRS LKNLILKNNQ IRSLTKYF L QDAFQLRYLD LSSNKIQMIQ KTSFPENVLN NLKMLLLHHN RFLCTCDAVW FVWWVQHTEV TIPYLATDVT CVGPGAHKG QSVISLDLYT CELDLTNEFL VPR

UniProtKB: Toll-like receptor 7

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Macromolecule #2: RNA (5'-R(*(OMG)P*UP*C)-3')

MacromoleculeName: RNA (5'-R(*(OMG)P*UP*C)-3') / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 925.622 Da
SequenceString:
(OMG)UC

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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: 6 / 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

BufferpH: 5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 197674
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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