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- PDB-9yot: Cryo-EM structure of an inactive dimer of the C. elegans EGFR (LE... -

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Basic information

Entry
Database: PDB / ID: 9yot
TitleCryo-EM structure of an inactive dimer of the C. elegans EGFR (LET-23) extracellular region bound to LIN-3.
Components
  • Protein spitz,Protein lin-3,Protein lin-3
  • Receptor tyrosine-protein kinase let-23
KeywordsSIGNALING PROTEIN / Receptor Tyrosine Kinase / epidermal growth factor receptor / ligand-bound dimer
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)
Drosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsZuo, Y. / Han, L. / Ferguson, K.M.
Funding support United States, 1items
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, H.T. / Walker, K. / Han, L. / Sternberg, P.W. / Ferguson, K.M.
History
DepositionOct 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor tyrosine-protein kinase let-23
C: Protein spitz,Protein lin-3,Protein lin-3
B: Receptor tyrosine-protein kinase let-23
D: Protein spitz,Protein lin-3,Protein lin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,12318
Polymers205,6974
Non-polymers6,42614
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Receptor tyrosine-protein kinase let-23 / Lethal protein 23


Mass: 91067.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Extracellular region (aa 27-819) of C. elegans EGFR, LET-23, with a C-terminal 6x-His tag
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: let-23, kin-7, ZK1067.1 / Plasmid: pFastBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P24348, receptor protein-tyrosine kinase
#2: Protein Protein spitz,Protein lin-3,Protein lin-3 / Abnormal cell lineage protein 3 / Lethal protein 94


Mass: 11781.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Drosophila melanogaster (fruit fly), (gene. exp.) Caenorhabditis elegans (invertebrata)
Gene: spi, CG10334, lin-3, let-94, F36H1.4 / Plasmid: PMT / Cell line (production host): SCHNEIDER 2(S2) CELLS / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q03345

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Sugars , 4 types, 14 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Inactive dimer of the C. elegans EGFR (LET-23) extracellular region bound to LIN-3.
Type: COMPLEX
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).
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Strain: Sf9 / Plasmid: pFastBac
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
12cryoSPARC3D reconstruction
13PHENIX1.21rc1_5127model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 267599 / Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 190.96 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002913344
ELECTRON MICROSCOPYf_angle_d0.549318014
ELECTRON MICROSCOPYf_chiral_restr0.04692040
ELECTRON MICROSCOPYf_plane_restr0.0032310
ELECTRON MICROSCOPYf_dihedral_angle_d13.3944870

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