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- EMDB-34091: TLR7 in complex with an inhibitor -

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Basic information

Entry
Database: EMDB / ID: EMD-34091
TitleTLR7 in complex with an inhibitor
Map data
Sample
  • Complex: TLR7 in complex with an inhibitor
    • Protein or peptide: Toll-like receptor 7
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2R,6R)-4-(8-cyanoquinolin-5-yl)-N-[(3S,4R)-4-fluoranylpyrrolidin-3-yl]-6-methyl-morpholine-2-carboxamide
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 / canonical NF-kappaB signal transduction / positive regulation of interferon-alpha production / 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 / canonical NF-kappaB signal transduction / positive regulation of interferon-alpha production / 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 non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / 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: 2.77 Å
AuthorsZhang Z / Ohto U / Shimizu T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: TLR7 in complex with an inhibitor
Authors: Zhang Z / Shimizu T
History
DepositionAug 15, 2022-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34091.png

Downloads & links

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Map

FileDownload / File: emd_34091.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.245 Å
Density
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.269882 - 0.40243375
Average (Standard dev.)0.00010288662 (±0.016879184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 199.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_34091_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34091_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34091_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TLR7 in complex with an inhibitor

EntireName: TLR7 in complex with an inhibitor
Components
  • Complex: TLR7 in complex with an inhibitor
    • Protein or peptide: Toll-like receptor 7
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2R,6R)-4-(8-cyanoquinolin-5-yl)-N-[(3S,4R)-4-fluoranylpyrrolidin-3-yl]-6-methyl-morpholine-2-carboxamide

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Supramolecule #1: TLR7 in complex with an inhibitor

SupramoleculeName: TLR7 in complex with an inhibitor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
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: 111.561273 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: MKLCILLAVV AFVGLSLGRS PWARWFPKTL PCDVTLDVSK NHVIVDCTDK HLTEIPGGIP TNTTNLTLTI NHIPDISPAS FHRLVHLVE IDFRCNCVPI RLGSKSNMCP RRLQIKPRSF SGLTYLKSLY LDGNQLLEIP QGLPPSLQLL SLEANNIFSI R KEQLTELA ...String:
MKLCILLAVV AFVGLSLGRS PWARWFPKTL PCDVTLDVSK NHVIVDCTDK HLTEIPGGIP TNTTNLTLTI NHIPDISPAS FHRLVHLVE IDFRCNCVPI RLGSKSNMCP RRLQIKPRSF SGLTYLKSLY LDGNQLLEIP QGLPPSLQLL SLEANNIFSI R KEQLTELA NIEILYLGQN CYYRNPCYVS YSIEKDAFLN LTKLKVLSLK DNNVTTVPTV LPSTLTELYL YNNMIAEIQE DD FNNLNQL QILDLSGNCP RCYNAPFPCT PCKNNSPLQI PVNAFDALTE LKVLRLHSNS LQHVPPRWFK NINNLQELDL SQN FLAKEI GDAKFLHFLP NLIQLDLSFN FELQVYRASM NLSQAFSSLK SLKILRIRGY VFKELKSFQL SPLHNLQNLE VLDL GTNFI KIANLSMFKQ FKRLKVIDLS VNKISPSGDS LVPRGSSNAR TSVESYEPQV LEQLYYFRYD KYARSCRFKN KEASF TSVQ ESCYKYGQTL DLSKNSIFFI KSSDFQHLSF LKCLNLSGNL ISQTLNGSEF QPLAELRYLD FSNNRLDLLH STAFEE LRK LEVLDISSNS HYFQSEGITH MLNFTKNLKV LQKLMMNDND ISSSTSRTME SESLRTLEFR GNHLDVLWRD GDNRYLQ LF KNLLKLEELD ISKNSLSFLP SGVFDGMPPN LKNLSLAKNG LKSFIWEKLR YLKNLETLDL SHNQLTTVPE RLSNCSRS L KNLILKNNQI RSLTKYFLQD AFQLRYLDLS SNKIQMIQKT SFPENVLNNL KMLLLHHNRF LCTCDAVWFV WWVQHTEVT IPYLATDVTC VGPGAHKGQS VISLDLYTCE LDLTNEFLVP RGSAAQHDEA VDNKFNKEQQ NAFYEILHLP NLNEEQRNAF IQSLKDDPS QSANLLAEAK KLNDAQAPKV DNKFNKEQQN AFYEILHLPN LNEEQRNAFI QSLKDDPSQS ANLLAEAKKL N DAQAPKVD ANSSSVP

UniProtKB: Toll-like receptor 7

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 10 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #4: (2R,6R)-4-(8-cyanoquinolin-5-yl)-N-[(3S,4R)-4-fluoranylpyrrolidin...

MacromoleculeName: (2R,6R)-4-(8-cyanoquinolin-5-yl)-N-[(3S,4R)-4-fluoranylpyrrolidin-3-yl]-6-methyl-morpholine-2-carboxamide
type: ligand / ID: 4 / Number of copies: 2 / Formula: JRI
Molecular weightTheoretical: 383.419 Da
Chemical component information

ChemComp-JRI:
(2R,6R)-4-(8-cyanoquinolin-5-yl)-N-[(3S,4R)-4-fluoranylpyrrolidin-3-yl]-6-methyl-morpholine-2-carboxamide

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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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 61.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 91789
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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