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- EMDB-30002: Cryo-EM structure of TLR7/Cpd-7 (DSR-139970) complex in open form -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-30002
TitleCryo-EM structure of TLR7/Cpd-7 (DSR-139970) complex in open form
Map data
Sample
  • Complex: TLR7/Cpd-7 (DSR-139970) complex
    • Protein or peptide: Toll-like receptor 7
  • Ligand: 2-ethoxy-8-(5-fluoranylpyridin-3-yl)-6-methyl-9-[[4-[[(1S,4S)-5-methyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]methyl]phenyl]methyl]purine
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 / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / positive regulation of type II interferon production / double-stranded RNA binding / defense response to virus / lysosome / single-stranded RNA binding / receptor complex / endosome / inflammatory response / innate immune response / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / 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: 2.8 Å
AuthorsZhang Z / Ohto U / Shimizu T
CitationJournal: Nat Commun / Year: 2020
Title: Structural analysis reveals TLR7 dynamics underlying antagonism.
Authors: Shingo Tojo / Zhikuan Zhang / Hiroyuki Matsui / Masahiro Tahara / Mitsunori Ikeguchi / Mami Kochi / Mami Kamada / Hideki Shigematsu / Akihisa Tsutsumi / Naruhiko Adachi / Takuma Shibata / ...Authors: Shingo Tojo / Zhikuan Zhang / Hiroyuki Matsui / Masahiro Tahara / Mitsunori Ikeguchi / Mami Kochi / Mami Kamada / Hideki Shigematsu / Akihisa Tsutsumi / Naruhiko Adachi / Takuma Shibata / Masaki Yamamoto / Masahide Kikkawa / Toshiya Senda / Yoshiaki Isobe / Umeharu Ohto / Toshiyuki Shimizu /
Abstract: Toll-like receptor 7 (TLR7) recognizes both microbial and endogenous RNAs and nucleosides. Aberrant activation of TLR7 has been implicated in several autoimmune diseases including systemic lupus ...Toll-like receptor 7 (TLR7) recognizes both microbial and endogenous RNAs and nucleosides. Aberrant activation of TLR7 has been implicated in several autoimmune diseases including systemic lupus erythematosus (SLE). Here, by modifying potent TLR7 agonists, we develop a series of TLR7-specific antagonists as promising therapeutic agents for SLE. These compounds protect mice against lethal autoimmunity. Combining crystallography and cryo-electron microscopy, we identify the open conformation of the receptor and reveal the structural equilibrium between open and closed conformations that underlies TLR7 antagonism, as well as the detailed mechanism by which TLR7-specific antagonists bind to their binding pocket in TLR7. Our work provides small-molecule TLR7-specific antagonists and suggests the TLR7-targeting strategy for treating autoimmune diseases.
History
DepositionFeb 6, 2020-
Header (metadata) releaseNov 11, 2020-
Map releaseNov 11, 2020-
UpdateNov 11, 2020-
Current statusNov 11, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6lw1
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30002.png

Downloads & links

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Map

FileDownload / File: emd_30002.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.996 Å
Density
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.17196889 - 0.2420572
Average (Standard dev.)0.00000729800 (±0.0067432844)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 219.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9960.9960.996
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z219.120219.120219.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.1720.2420.000

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Supplemental data

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Sample components

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Entire : TLR7/Cpd-7 (DSR-139970) complex

EntireName: TLR7/Cpd-7 (DSR-139970) complex
Components
  • Complex: TLR7/Cpd-7 (DSR-139970) complex
    • Protein or peptide: Toll-like receptor 7
  • Ligand: 2-ethoxy-8-(5-fluoranylpyridin-3-yl)-6-methyl-9-[[4-[[(1S,4S)-5-methyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]methyl]phenyl]methyl]purine

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Supramolecule #1: TLR7/Cpd-7 (DSR-139970) complex

SupramoleculeName: TLR7/Cpd-7 (DSR-139970) complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 200 KDa

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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

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Macromolecule #2: 2-ethoxy-8-(5-fluoranylpyridin-3-yl)-6-methyl-9-[[4-[[(1S,4S)-5-m...

MacromoleculeName: 2-ethoxy-8-(5-fluoranylpyridin-3-yl)-6-methyl-9-[[4-[[(1S,4S)-5-methyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]methyl]phenyl]methyl]purine
type: ligand / ID: 2 / Number of copies: 2 / Formula: EX3
Molecular weightTheoretical: 487.572 Da
Chemical component information

ChemComp-EX3:
2-ethoxy-8-(5-fluoranylpyridin-3-yl)-6-methyl-9-[[4-[[(1S,4S)-5-methyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]methyl]phenyl]methyl]purine

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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

Concentration0.8 mg/mL
BufferpH: 4.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 301212

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