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- EMDB-35258: Cryo-EM structure of TLR7/TH-407b complex -

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Basic information

Entry
Database: EMDB / ID: EMD-35258
TitleCryo-EM structure of TLR7/TH-407b complex
Map data
Sample
  • Complex: TLR7
    • Protein or peptide: Toll-like receptor 7
  • Ligand: (1S,3R)-5-[4-(8-nitroquinolin-5-yl)piperazin-1-yl]carbonyladamantan-2-one
KeywordsTLR7 / antagonist / IMMUNE SYSTEM
Function / homology
Function and homology information


toll-like receptor 7 signaling pathway / response to cGMP / siRNA binding / early phagosome / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / positive regulation of interferon-alpha production / canonical NF-kappaB signal transduction / positive regulation of chemokine production ...toll-like receptor 7 signaling pathway / response to cGMP / siRNA binding / early phagosome / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / 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 / regulation of protein phosphorylation / cellular response to virus / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / positive regulation of type II interferon production / double-stranded RNA binding / defense response to virus / single-stranded RNA binding / lysosome / receptor complex / endosome / 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 / Leucine-rich repeat, SDS22-like subfamily / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / 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 / Leucine-rich repeat, SDS22-like subfamily / TIR domain profile. / 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 7
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of TLR7/TH-407b complex
Authors: Zhang Z / Yin H / Shimizu T
History
DepositionFeb 6, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_35258.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.162 Å
Density
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.22707991 - 0.3138586
Average (Standard dev.)-0.0000064984265 (±0.0076278653)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 232.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : TLR7

EntireName: TLR7
Components
  • Complex: TLR7
    • Protein or peptide: Toll-like receptor 7
  • Ligand: (1S,3R)-5-[4-(8-nitroquinolin-5-yl)piperazin-1-yl]carbonyladamantan-2-one

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Supramolecule #1: TLR7

SupramoleculeName: TLR7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: (1S,3R)-5-[4-(8-nitroquinolin-5-yl)piperazin-1-yl]carbonyladamant...

MacromoleculeName: (1S,3R)-5-[4-(8-nitroquinolin-5-yl)piperazin-1-yl]carbonyladamantan-2-one
type: ligand / ID: 2 / Number of copies: 2 / Formula: GJX
Molecular weightTheoretical: 434.488 Da

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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: 4.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 57.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.84 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5gmh

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 337415
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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