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- EMDB-11982: Cryo-EM of Aedes Aegypti Toll5A dimer bound to Spz1C -

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Basic information

Entry
Database: EMDB / ID: EMD-11982
TitleCryo-EM of Aedes Aegypti Toll5A dimer bound to Spz1C
Map dataEM map
Sample
  • Complex: Cryo-EM of Aedes Aegypti Toll5A dimer bound to Spz1C
    • Complex: Toll-like receptor
      • Protein or peptide: Toll-like receptor
    • Complex: AAEL013433-PA
      • Protein or peptide: AAEL013433-PA
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


toll-like receptor signaling pathway / transmembrane signaling receptor activity / immune response / extracellular space / membrane
Similarity search - Function
Spaetzle / Spaetzle / Toll-like receptor / TIR domain / Leucine-rich repeats, bacterial type / Toll - interleukin 1 - resistance / Leucine-rich repeat, SDS22-like subfamily / Cystine-knot cytokine / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain ...Spaetzle / Spaetzle / Toll-like receptor / TIR domain / Leucine-rich repeats, bacterial type / Toll - interleukin 1 - resistance / Leucine-rich repeat, SDS22-like subfamily / Cystine-knot cytokine / 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
TIR domain-containing protein / AAEL013433-PA
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.23 Å
AuthorsGangloff M / Hardwick SW / Chirgadze DY
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/P02260X/1 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Structure and dynamics of Toll immunoreceptor activation in the mosquito Aedes aegypti.
Authors: Yoann Saucereau / Thomas H Wilson / Matthew C K Tang / Martin C Moncrieffe / Steven W Hardwick / Dimitri Y Chirgadze / Sandro G Soares / Maria Jose Marcaida / Nicholas J Gay / Monique Gangloff /
Abstract: Aedes aegypti has evolved to become an efficient vector for arboviruses but the mechanisms of host-pathogen tolerance are unknown. Immunoreceptor Toll and its ligand Spaetzle have undergone ...Aedes aegypti has evolved to become an efficient vector for arboviruses but the mechanisms of host-pathogen tolerance are unknown. Immunoreceptor Toll and its ligand Spaetzle have undergone duplication which may allow neofunctionalization and adaptation. Here we present cryo-EM structures and biophysical characterisation of low affinity Toll5A complexes that display transient but specific interactions with Spaetzle1C, forming asymmetric complexes, with only one ligand clearly resolved. Loop structures of Spaetzle1C and Toll5A intercalate, temporarily bridging the receptor C-termini to promote signalling. By contrast unbound receptors form head-to-head homodimers that keep the juxtamembrane regions far apart in an inactive conformation. Interestingly the transcriptional signature of Spaetzle1C differs from other Spaetzle cytokines and controls genes involved in innate immunity, metabolism and tissue regeneration. Taken together our results explain how upregulation of Spaetzle1C in the midgut and Toll5A in the salivary gland shape the concomitant immune response.
History
DepositionNov 24, 2020-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateJan 25, 2023-
Current statusJan 25, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_11982.png

Downloads & links

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Map

FileDownload / File: emd_11982.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.033301696 - 0.23375507
Average (Standard dev.)0.0007686079 (±0.010843067)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 315.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map

Fileemd_11982_half_map_1.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_11982_half_map_2.map
AnnotationHalf 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 : Cryo-EM of Aedes Aegypti Toll5A dimer bound to Spz1C

EntireName: Cryo-EM of Aedes Aegypti Toll5A dimer bound to Spz1C
Components
  • Complex: Cryo-EM of Aedes Aegypti Toll5A dimer bound to Spz1C
    • Complex: Toll-like receptor
      • Protein or peptide: Toll-like receptor
    • Complex: AAEL013433-PA
      • Protein or peptide: AAEL013433-PA
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM of Aedes Aegypti Toll5A dimer bound to Spz1C

SupramoleculeName: Cryo-EM of Aedes Aegypti Toll5A dimer bound to Spz1C / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 230 KDa

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Supramolecule #2: Toll-like receptor

SupramoleculeName: Toll-like receptor / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Aedes aegypti (yellow fever mosquito)

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Supramolecule #3: AAEL013433-PA

SupramoleculeName: AAEL013433-PA / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Aedes aegypti (yellow fever mosquito)

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Macromolecule #1: Toll-like receptor

MacromoleculeName: Toll-like receptor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Aedes aegypti (yellow fever mosquito)
Molecular weightTheoretical: 87.675773 KDa
Recombinant expressionOrganism: Drosophila melanocephala (fry)
SequenceString: TSTKRFTCPE ESEASNCSCE EFPSKTHFYC PDFNPTLYVD VEDRMRVDFK CYDEPHDFKS LPNLAIGSVK LLTVVDCVLD DDRPILESF KFLEVADVRS FVYNNHENGI RYNAKYFEGM EQLENLTLAR GVVSIDRDTF SGFLNLKRLT IEHNKLNLQP G TFEALSNL ...String:
TSTKRFTCPE ESEASNCSCE EFPSKTHFYC PDFNPTLYVD VEDRMRVDFK CYDEPHDFKS LPNLAIGSVK LLTVVDCVLD DDRPILESF KFLEVADVRS FVYNNHENGI RYNAKYFEGM EQLENLTLAR GVVSIDRDTF SGFLNLKRLT IEHNKLNLQP G TFEALSNL TYLGLVYNGL NEIQPGLFDG LESLEALSLS YNDIKSLSAG SFNGLSSLRM LNLRVNKIES FDANTFASLK EL SRLEITL NPFVSLPRGL FSENKKLKTL ILTNNRKLVT LPEELLANLK ELTVVNLSHN GVGNLPESLL SGSSGIIELN LGY NRLNSL PEELLSDQPQ LQVLNLDHNQ LESIPDYFLE RNVELQTLYL SHNRLRSLSE KAFTKLKNLK ELHLENNQLQ TIPQ FLFSG TPKLEEIYMQ NNQLALHANS FINEELSIAD NDNTPFQVLQ KLRILHLRNN SISTIFQDWY INNLEMQSLD LSFNK LPGL SYTQLQFQSN ITLNLSNNEI SQVLLIDDLD LQPYQRINVD LNHNPLNCNC NALKFIQLIQ SKAEHGLQFN VDQLRC SEP PNLLDATMDQ LQTKDLLCDF ESADDCPKDC QCAMRLLDHT VIVNCSGRGL TEFPDLPIPS QLHEDFNALE VHVENNR LT KLPNLTKHNE ITQLYARNNS IQNLLPHNIP SKLRIIDLSQ NLLKMIDDST LAQINRSSHL ETIRLSQNQW LCDCPASS F LIFVQQNSRL ISDMSAIRCH PSGKSLDSIT VNELCFEDYT TENLYFQ

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Macromolecule #2: AAEL013433-PA

MacromoleculeName: AAEL013433-PA / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Aedes aegypti (yellow fever mosquito)
Molecular weightTheoretical: 12.941044 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString:
SDTANAPFLC ESEQLLIHPK EELSRNNSMV WIVNTKDYKQ GVRIEKCLKR QLGKPCNFCD ADTECKQLFH YRTLVAVDKV TKKPYKEQV LLPSCCKCAK ILSTGWSHPQ FEK

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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: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMNaClSodium chloridesodium chloride
50.0 mMC4H11NO3Tris-HClTris
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I / Details: Blotting force 0.

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 51.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 507268
Startup modelType of model: INSILICO MODEL / Details: molecular replacement
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 40153
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4lxr

chain_id: A

4lxr

chain_id: J

4lxr

chain_id: K
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7b1b:
Cryo-EM of Aedes Aegypti Toll5A dimer bound to Spz1C

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