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- EMDB-40786: Structural basis and functional roles for Toll-like receptor bind... -

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Basic information

Entry
Database: EMDB / ID: EMD-40786
TitleStructural basis and functional roles for Toll-like receptor binding to Latrophilin adhesion-GPCR in embryo development
Map dataPostprocessed map
Sample
  • Complex: The binary complex of C. elegans TOL-1 with C. elegans LAT-1 extracellular domains
    • Protein or peptide: Toll-like receptor 1/TOL-1
    • Protein or peptide: Latrophilin 1/LAT-1
Keywordssynapse / C. elegans / ADGR / GPCR / CELL ADHESION
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsLi J / Rosas GC / Arac D / Ozkan E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 GM148412 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis and functional roles for Toll-like receptor binding to Latrophilin in C. elegans development.
Authors: Gabriel Carmona-Rosas / Jingxian Li / Jayson J Smith / Wioletta I Nawrocka / Shouqiang Cheng / Elana E Baltrusaitis / Minglei Zhao / Demet Araç / Paschalis Kratsios / Engin Özkan /
Abstract: Latrophilins are conserved adhesion-type G-protein-coupled receptors associated with embryonic defects and lethality. However, their mechanistic roles and ligands in embryogenesis remain unknown. ...Latrophilins are conserved adhesion-type G-protein-coupled receptors associated with embryonic defects and lethality. However, their mechanistic roles and ligands in embryogenesis remain unknown. Here, we identified TOL-1, the sole Toll-like receptor in Caenorhabditis elegans, as a ligand for the C. elegans latrophilin, LAT-1. The extracellular lectin domain of LAT-1 directly binds to the second leucine-rich repeat domain of TOL-1. The crystal structure and cryo-electron microscopy density map of the LAT-1-TOL-1 extracellular region complex reveal a one-to-one lectin domain interaction with the convex face of a leucine-rich repeat domain. In C. elegans, endogenous mRNA and protein localization analyses showed mutually exclusive sites of expression, suggesting that in vivo LAT-1-TOL-1 interactions mostly occur in trans. Mutagenesis of key interface residues that disrupt the LAT-1-TOL-1 interaction led to partial lethality and malformed embryos. Thus, TOL-1 binding to LAT-1 represents a receptor-ligand axis essential for animal development.
History
DepositionMay 16, 2023-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40786.png

Downloads & links

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Map

FileDownload / File: emd_40786.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 272.128 Å		1.06 Å/pix.
x 256 pix.
= 272.128 Å		1.06 Å/pix.
x 256 pix.
= 272.128 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.012612101 - 0.03890138
Average (Standard dev.)0.000075810705 (±0.0017290576)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 272.128 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Halp map 1

Fileemd_40786_half_map_1.map
AnnotationHalp map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_40786_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The binary complex of C. elegans TOL-1 with C. elegans LAT-1 extr...

EntireName: The binary complex of C. elegans TOL-1 with C. elegans LAT-1 extracellular domains
Components
  • Complex: The binary complex of C. elegans TOL-1 with C. elegans LAT-1 extracellular domains
    • Protein or peptide: Toll-like receptor 1/TOL-1
    • Protein or peptide: Latrophilin 1/LAT-1

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Supramolecule #1: The binary complex of C. elegans TOL-1 with C. elegans LAT-1 extr...

SupramoleculeName: The binary complex of C. elegans TOL-1 with C. elegans LAT-1 extracellular domains
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The Binary complex includes C.elegans Toll-like receptor 1 (Tol-1) and C. elegans Latrophilin 1 (LAT-1).
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 172 KDa

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Macromolecule #1: Toll-like receptor 1/TOL-1

MacromoleculeName: Toll-like receptor 1/TOL-1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: ADPHHHHHHG SGLNDIFEAQ KIEWHEADPG YTDECPKFCK CAPDPVQPTS KLLLCDYSSK NTTITPIASS NYDQVANIRS LFISCDNNNF QFPDAYFKSL TALHHLRIVG CETTHFSVKL FEDLAALRRL ELDQISTAST SFEMTEDVLM PLARLEKFSL TRSRNIELPQ ...String:
ADPHHHHHHG SGLNDIFEAQ KIEWHEADPG YTDECPKFCK CAPDPVQPTS KLLLCDYSSK NTTITPIASS NYDQVANIRS LFISCDNNNF QFPDAYFKSL TALHHLRIVG CETTHFSVKL FEDLAALRRL ELDQISTAST SFEMTEDVLM PLARLEKFSL TRSRNIELPQ RLLCSLPHLQ VLNISSNELP SLRREESCVA QQLLIVDLSR NRLTNIEQFL RGIPAIRQIS VAYNSIAELD LSLATPFLQQ LDAEANRIVD LTSLPGTVVH VNLAGNALKR VPDAVAELAS LVALNVSRNE IEAGNSSVFS SPELEMLDAS YNKLDSLPVE WLQKCEKRIA HLHLEHNSIE QLTGGVLANA TNLQTLDLSS NQLRVFRDEV LPENSKIGNL RLSNNSLELL EPSSLSGLKL ESLDLSHNKL TEVPAAIGKV EQLKKVDLSH NRIAKVYQYV LNKIKQLHTV DLSNNQLQSI GPYIFSDSSE LHSLDVSNNE ISLLFKDAFA RCPKLRKISM KMNKIKSLDE GLTEASGLRR LDVSHNEILV LKWSALPENL EILNADNNDI NLLTAASMSP STANLKSVSL SNNGITIMNA DQIPNSLESL DVSNNRLAKL GKTALAAKSQ LRRLNLKGNL LTVVATESMK VVEAVHPLKV EISENPLICD CQMGWMIGGA KPKVLIQDSE TASCSHAVDG HQIQIQSLSK KDLLCPYKSV CEPECICCQY GNCDCKSVCP ANCRCFRDDQ FNINIVRCHG NSSMVPKREF VVSELPVSAT EIILSGVTLP QLRTHSFIGR LRLQRLHING TGLRSIQPKA FHTLPALKTL DLSDNSLISL SGEEFLKCGE VSQLFLNGNR FSTLSRGIFE KLPNLKYLTL HNNSLEDIPQ VLHSTALSKI SLSSNPLRCD CSGGSQQHLH HRRDPKAHPF WEHNAAEWFS LHRHLVVDFP KVECWENVTK AFLTNDTTVL SAYPPNMGND VFVMPIEEFL RDYNSTICVP FSSGFFGQDP QNSDIQH

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Macromolecule #2: Latrophilin 1/LAT-1

MacromoleculeName: Latrophilin 1/LAT-1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: AVPSNKPTTD ESGTISHTIC DGEAAELSCP AGKVISIVLG NYGRFSVAVC LPDNDIVPSN INCQNHKTKS ILEKKCNGDS MCYFTVDKKT FTEDPCPNTP KYLEVKYNCV VPATTTTTTT TTSTTTTDSS LIVDEEEEAQ KDALNSDVIK PVKKKEDVFC SATNRRGVNW ...String:
AVPSNKPTTD ESGTISHTIC DGEAAELSCP AGKVISIVLG NYGRFSVAVC LPDNDIVPSN INCQNHKTKS ILEKKCNGDS MCYFTVDKKT FTEDPCPNTP KYLEVKYNCV VPATTTTTTT TTSTTTTDSS LIVDEEEEAQ KDALNSDVIK PVKKKEDVFC SATNRRGVNW QNTKSGTTSS APCPEGSSGK QLWACTEEGQ WLTEFPNSAG CESNWISSRN SVLSGVISSE DVSGLPEFLR NLGSETRRPM VGGDLPKVLH LLEKTVNVIA EESWAYQHLP LSNKGAVEVM NYMLRNQEIW GSWDVTKRKE FASRFILAAE KAMVASAKGM MTSAESNVIV QPAITVEISH KIKMSSQPTD YILFPSAALW NGQNVDNVNI PRDAILKINK DETQVFFSSF DNLGAQMTPS DVTVAIAGTD QTEVRKRRVV SRIVGASLIE NGKERRVENL TQPVRITFYH KESSVRHLSN PTCVWWNHHE LKWKPSGCKL SYHNKTMTSC DCTHLTHFAV LMDVRGHDLN EIDQTLLTHH HHHH

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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

Concentration0.28 mg/mL
BufferpH: 8.5 / Details: 10 mM Tris, pH 8.5, 150 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 3333 / Average exposure time: 4.2 sec. / Average electron dose: 60.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION / Details: CTF correction was done in Relion reconstruction / Type: PHASE FLIPPING ONLY
Startup modelType of model: OTHER / Details: Initial model was generated in Relion.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 144253
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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