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- PDB-9hkt: Drosophila melanogaster insulin receptor ectodomain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9hkt
TitleDrosophila melanogaster insulin receptor ectodomain in complex with one DILP2 molecule
Components
  • (Probable insulin-like peptide 2) x 2
  • Insulin-like receptor
KeywordsSIGNALING PROTEIN / Receptor / Dilp2 / Drosophila / complex
Function / homology
Function and homology information


primary spermatocyte growth / negative regulation of peptide hormone secretion / Extra-nuclear estrogen signaling / response to anoxia / negative regulation of entry into reproductive diapause / Insulin signaling pathway / Insulin receptor recycling / female mating behavior / embryonic development via the syncytial blastoderm / larval feeding behavior ...primary spermatocyte growth / negative regulation of peptide hormone secretion / Extra-nuclear estrogen signaling / response to anoxia / negative regulation of entry into reproductive diapause / Insulin signaling pathway / Insulin receptor recycling / female mating behavior / embryonic development via the syncytial blastoderm / larval feeding behavior / male germ-line stem cell asymmetric division / female germ-line stem cell population maintenance / germ-band shortening / germ-line stem-cell niche homeostasis / imaginal disc growth / carbohydrate homeostasis / open tracheal system development / germ-line stem cell division / negative regulation of circadian sleep/wake cycle, sleep / positive regulation of neuron remodeling / lymph gland development / follicle cell of egg chamber development / positive regulation of border follicle cell migration / female germ-line stem cell asymmetric division / positive regulation of fat cell proliferation / regulation of growth rate / intestinal stem cell homeostasis / growth cone membrane / positive regulation of organ growth / response to amino acid starvation / positive regulation of lipid storage / insulin receptor complex / regulation of organ growth / insulin receptor activity / embryo development ending in birth or egg hatching / positive regulation of multicellular organism growth / sleep / insulin binding / triglyceride homeostasis / negative regulation of glycogen catabolic process / regulation of cell size / negative regulation of feeding behavior / positive regulation of neuroblast proliferation / response to food / negative regulation of macroautophagy / positive regulation of wound healing / locomotor rhythm / female gonad development / lipid homeostasis / insulin receptor substrate binding / regulation of multicellular organism growth / positive regulation of cell size / developmental growth / phosphatidylinositol 3-kinase binding / positive regulation of TORC1 signaling / cholesterol homeostasis / axon guidance / cellular response to starvation / insulin receptor binding / determination of adult lifespan / growth factor activity / response to cocaine / locomotory behavior / cellular response to glucose stimulus / hormone activity / circadian rhythm / receptor protein-tyrosine kinase / SH3 domain binding / multicellular organism growth / insulin receptor signaling pathway / protein autophosphorylation / nervous system development / regulation of cell population proliferation / glucose homeostasis / positive regulation of cell growth / protein tyrosine kinase activity / response to oxidative stress / protein phosphorylation / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / axon / positive regulation of cell population proliferation / : / extracellular region / ATP binding / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Long hematopoietin receptor, single chain family signature. / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily ...Long hematopoietin receptor, single chain family signature. / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / 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 / Fibronectin type III domain / Growth factor receptor cysteine-rich domain superfamily / : / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / 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. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Insulin-like receptor / Insulin-like peptide 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsShafi, T. / Moroz, O.V. / Jenkins, H.T. / Chechik, M. / Isupov, M.N. / Brzozowski, A.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W003783/1 United Kingdom
CitationJournal: To Be Published
Title: Drosophila melanogaster insulin receptor ectodomain in complex with DILP2
Authors: Shafi, T. / Moroz, O.V. / Jenkins, H.T. / Chechik, M. / Isupov, M.N. / Brzozowski, A.M.
History
DepositionDec 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 6, 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: Insulin-like receptor
B: Insulin-like receptor
G: Probable insulin-like peptide 2
H: Probable insulin-like peptide 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,38325
Polymers245,9254
Non-polymers5,45821
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

#1: Protein Insulin-like receptor / dIR / dInr / dIRH


Mass: 120074.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: InR, dinr, Dir-a, Inr-a, CG18402 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P09208, receptor protein-tyrosine kinase
#2: Protein/peptide Probable insulin-like peptide 2 / dILP2 / Insulin-related peptide 2


Mass: 3025.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VT51
#3: Protein/peptide Probable insulin-like peptide 2 / dILP2 / Insulin-related peptide 2


Mass: 2750.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VT51
#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.: 4
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: 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.: 17 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
Has ligand of interestY
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: Drosophila insulin receptor ectodomain with DILP-2 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.25 MDa / Experimental value: NO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5 / Details: 20mM Hepes pH 7.5, 200mM NaCl
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: the receptor ectodomain was mixed with Dilp2 in 1:40 ratio
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: REFMAC / Version: 5.8.0267 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 882882 / Details: Topaz picking > Extract with fom -3
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127081 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingPDB-ID: 8cls

8cls


Accession code: 8cls / Source name: PDB / Type: experimental model
RefinementResolution: 3.7→371.95 Å / Cor.coef. Fo:Fc: 0.814 / SU B: 23.363 / SU ML: 0.304 / ESU R: 0.142
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.46258 --
obs0.46258 2127659 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 120.068 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å21.3 Å2-0.31 Å2
2---4.47 Å22.04 Å2
3---2.21 Å2
Refinement stepCycle: 1 / Total: 14222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0030.01214567
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.0251.68119766
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.24851739
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.71722.913745
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.487152530
ELECTRON MICROSCOPYr_dihedral_angle_4_deg12.5161584
ELECTRON MICROSCOPYr_chiral_restr0.080.21967
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.0210899
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it2.39811.7126983
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it4.43817.5568713
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it2.34112.2487584
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined10.63620382
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.7→3.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.632 158298 -
obs--100 %

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