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- EMDB-73277: Cryo-EM structure of an inactive dimer of the C. elegans EGFR (LE... -

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Basic information

Entry
Database: EMDB / ID: EMD-73277
TitleCryo-EM structure of an inactive dimer of the C. elegans EGFR (LET-23) extracellular region bound to LIN-3.
Map data
Sample
  • Complex: Inactive 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,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 / 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 ...inductive cell-cell signaling / 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 / Signaling by ERBB2 / Extra-nuclear estrogen signaling / Drug-mediated inhibition of ERBB2 signaling / 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 / RAF/MAP kinase cascade / EGFR downregulation / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / vulval development / positive regulation of ovulation / nematode larval development / ovulation / egg-laying behavior / male genitalia development / regulation of cell fate specification / sleep / epidermal growth factor receptor activity / 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 / signaling receptor complex / apical plasma membrane / receptor ligand activity / regulation of DNA-templated transcription / lipid binding / negative regulation of apoptotic process / : / ATP binding / membrane / plasma membrane
Similarity search - Function
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. ...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 lin-3
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 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_73277.png

Downloads & links

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Map

FileDownload / File: emd_73277.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-0.23170957 - 0.5786081
Average (Standard dev.)0.0000424448 (±0.0073332046)
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_73277_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_73277_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Inactive dimer of the C. elegans EGFR (LET-23) extracellular regi...

EntireName: Inactive dimer of the C. elegans EGFR (LET-23) extracellular region bound to LIN-3.
Components
  • Complex: Inactive 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,Protein lin-3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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

SupramoleculeName: Inactive 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,Protein lin-3

MacromoleculeName: Protein spitz,Protein lin-3,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 lin-3

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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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: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 267599
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9yot:
Cryo-EM structure of an inactive dimer of the C. elegans EGFR (LET-23) extracellular region bound to LIN-3.

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