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- EMDB-73276: Cryo-EM structure of an active dimer of the C. elegans EGFR (LET-... -

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Basic information

Entry
Database: EMDB / ID: EMD-73276
TitleCryo-EM structure of an active dimer of the C. elegans EGFR (LET-23) extracellular region bound to LIN-3
Map data
Sample
  • Complex: Active dimer of the C. elegans EGFR (LET-23) extracellular region bound to LIN-3
    • Protein or peptide: Receptor tyrosine-protein kinase let-23
    • Protein or peptide: Protein spitz,Protein lin-3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsReceptor Tyrosine Kinase / epidermal growth factor receptor / ligand-bound dimer / SIGNALING PROTEIN
Function / homology
Function and homology information


inductive cell-cell signaling / ectodermal cell fate determination / stomatogastric nervous system development / stem cell fate commitment / photoreceptor cell fate determination / photoreceptor cell differentiation / vulval cell fate specification / SHC1 events in ERBB2 signaling / Nuclear signaling by ERBB4 / Signaling by EGFR ...inductive cell-cell signaling / ectodermal cell fate determination / stomatogastric nervous system development / stem cell fate commitment / photoreceptor cell fate determination / photoreceptor cell differentiation / vulval cell fate specification / SHC1 events in ERBB2 signaling / Nuclear signaling by ERBB4 / Signaling by EGFR / GAB1 signalosome / EGFR interacts with phospholipase C-gamma / Sema4D induced cell migration and growth-cone collapse / ERBB2 Regulates Cell Motility / ERBB2 Activates PTK6 Signaling / epithelial cell proliferation involved in Malpighian tubule morphogenesis / Signaling by ERBB2 / Extra-nuclear estrogen signaling / Drug-mediated inhibition of ERBB2 signaling / determination of genital disc primordium / Signal transduction by L1 / positive regulation of vulval development / Downregulation of ERBB4 signaling / PIP3 activates AKT signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / PI3K events in ERBB2 signaling / EGFR Transactivation by Gastrin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Downregulation of ERBB2 signaling / ommatidial rotation / oenocyte development / RAF/MAP kinase cascade / EGFR downregulation / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / vulval development / dorsal closure / positive regulation of ovulation / spiracle morphogenesis, open tracheal system / nematode larval development / ovulation / egg-laying behavior / border follicle cell migration / positive regulation of border follicle cell migration / imaginal disc-derived wing morphogenesis / male genitalia development / peripheral nervous system development / regulation of cell fate specification / heart process / olfactory learning / behavioral response to ethanol / sleep / positive regulation of neurogenesis / epidermal growth factor receptor activity / epidermal growth factor receptor binding / uterus development / lateral plasma membrane / post-embryonic development / transmembrane receptor protein tyrosine kinase activity / positive regulation of epithelial cell proliferation / basal plasma membrane / molecular function activator activity / growth factor activity / receptor protein-tyrosine kinase / epidermal growth factor receptor signaling pathway / neuron differentiation / cell-cell junction / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / basolateral plasma membrane / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / signaling receptor complex / cell surface receptor signaling pathway / apical plasma membrane / receptor ligand activity / negative regulation of gene expression / Golgi membrane / positive regulation of cell population proliferation / regulation of DNA-templated transcription / lipid binding / negative regulation of apoptotic process / endoplasmic reticulum membrane / endoplasmic reticulum / : / ATP binding / membrane / plasma membrane
Similarity search - Function
Protein Gurken/Spitz / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats ...Protein Gurken/Spitz / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor tyrosine-protein kinase let-23 / Protein spitz / Protein lin-3
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.37 Å
AuthorsZuo Y / Han L / Ferguson KM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM149406 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: Ligand regulation and function of preformed EGFR dimers
Authors: Zuo Y / Schwartz HT / Walker K / Han L / Sternberg PW / Ferguson KM
History
DepositionOct 13, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73276.png

Downloads & links

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Map

FileDownload / File: emd_73276.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.18443798 - 0.57014763
Average (Standard dev.)0.000038433438 (±0.0073890947)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73276_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_73276_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Active dimer of the C. elegans EGFR (LET-23) extracellular region...

EntireName: Active dimer of the C. elegans EGFR (LET-23) extracellular region bound to LIN-3
Components
  • Complex: Active dimer of the C. elegans EGFR (LET-23) extracellular region bound to LIN-3
    • Protein or peptide: Receptor tyrosine-protein kinase let-23
    • Protein or peptide: Protein spitz,Protein lin-3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Active dimer of the C. elegans EGFR (LET-23) extracellular region...

SupramoleculeName: Active dimer of the C. elegans EGFR (LET-23) extracellular region bound to LIN-3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Extracellular region (aa 27-819) of C. elegans EGFR, LET-23, with a C-terminal 6x-His tag bound to the EGF domain of LIN-3 (aa K148-N206), with an N-terminal fusion comprising (i) an Arg, ...Details: Extracellular region (aa 27-819) of C. elegans EGFR, LET-23, with a C-terminal 6x-His tag bound to the EGF domain of LIN-3 (aa K148-N206), with an N-terminal fusion comprising (i) an Arg, (ii) 6xHis tag (iii) aa 44-79 of Drosophila melanogaster SPITZ (Q01083) and (iv) a Factor Xa cleavage site (IEDGR).
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Receptor tyrosine-protein kinase let-23

MacromoleculeName: Receptor tyrosine-protein kinase let-23 / type: protein_or_peptide / ID: 1
Details: Extracellular region (aa 27-819) of C. elegans EGFR, LET-23, with a C-terminal 6x-His tag
Number of copies: 2 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 91.067219 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: QLWKRCVSPQ DCLCSGTTNG ISRYGTGNIL EDLETMYRGC RRVYGNLEIT WIEANEIKKW RESTNSTVDP KNEDSPLKSI NFFDNLEEI RGSLIIYRAN IQKISFPRLR VIYGDEVFHD NALYIHKNDK VHEVVMRELR VIRNGSVTIQ DNPKMCYIGD K IDWKELLY ...String:
QLWKRCVSPQ DCLCSGTTNG ISRYGTGNIL EDLETMYRGC RRVYGNLEIT WIEANEIKKW RESTNSTVDP KNEDSPLKSI NFFDNLEEI RGSLIIYRAN IQKISFPRLR VIYGDEVFHD NALYIHKNDK VHEVVMRELR VIRNGSVTIQ DNPKMCYIGD K IDWKELLY DPDVQKVETT NSHQHCYQNG KSMAKCHESC NDKCWGSGDN DCQRVYRSVC PKSCSQCFYS NSTSSYECCD SA CLGGCTG HGPKNCIACS KYELDGICIE TCPSRKIFNH KTGRLVFNPD GRYQNGNHCV KECPPELLIE NDVCVRHCSD GHH YDATKD VRECEKCRSS SCPKICTVDG HLTNETLKNL EGCEQIDGHL IIEHAFTYEQ LKVLETVKIV SEYITIVQQN FYDL KFLKN LQIIEGRKLH NVRWALAIYQ CDDLEELSLN SLKLIKTGAV LIMKNHRLCY VSKIDWSSII TSKGKDNKPS LAIAE NRDS KLCETEQRVC DKNCNKRGCW GKEPEDCLEC KTWKSVGTCV EKCDTKGFLR NQTSMKCERC SPECETCNGL GELDCL TCR HKTLYNSDFG NRMECVHDCP VSHFPTQKNV CEKCHPTCYD NGCTGPDSNL GYGGCKQCKY AVKYENDTIF CLQSSGM NN VCVENDLPNY YISTYDTEGV IETHCEKCSI SCKTCSSAGR NVVQNKCVCK HVEYQPNPSE RICMDQCPVN SFMVPDTN N TVCKKCHHEC DQNYHCANGQ STGCQKCKNF TVFKGDIAQC VSECPKNLPF SNPANGECLD YDIASRQRKT RMHHHHHH

UniProtKB: Receptor tyrosine-protein kinase let-23

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Macromolecule #2: Protein spitz,Protein lin-3

MacromoleculeName: Protein spitz,Protein lin-3 / type: protein_or_peptide / ID: 2
Details: The EGF domain of LIN-3 (aa K148-N206) follows an N-terminal fusion comprising (i) an Arg, (ii) 6xHis tag (iii) aa 44-79 of Drosophila melanogaster SPITZ (Q01083) and (iv) a Factor Xa ...Details: The EGF domain of LIN-3 (aa K148-N206) follows an N-terminal fusion comprising (i) an Arg, (ii) 6xHis tag (iii) aa 44-79 of Drosophila melanogaster SPITZ (Q01083) and (iv) a Factor Xa cleavage site (IEDGR). See PMID 26060020.,The EGF domain of LIN-3 (aa K148-N206) follows an N-terminal fusion comprising (i) an Arg, (ii) 6xHis tag (iii) aa 44-79 of Drosophila melanogaster SPITZ (Q01083) and (iv) a Factor Xa cleavage site (IEDGR). See PMID 26060020.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 11.781285 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString:
RHHHHHHSMS GTALPPTQAP VTSSTTMRTT TTTTPRPNIT IEGRSKLKEA KCKDYCHHNA TCHVEVIFRE DRVSAVVPSC HCPQGWEGT RCDRHYVQAF YAPIN

UniProtKB: Protein spitz, Protein lin-3

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

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

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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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 285565
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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