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- PDB-9ef4: Cryo-EM structure of Drosophila melanogaster insulin receptor (dm... -

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Basic information

Entry
Database: PDB / ID: 9ef4
TitleCryo-EM structure of Drosophila melanogaster insulin receptor (dmIR) bound with two DILP1, symmetric conformation
Components
  • DILP1 A-chain
  • DILP1 B-chain
  • Insulin-like receptor
KeywordsSTRUCTURAL PROTEIN / Insulin receptor / DILP
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 / male germ-line stem cell asymmetric division ...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 / male germ-line stem cell asymmetric division / female germ-line stem cell population maintenance / germ-band shortening / carbohydrate homeostasis / germ-line stem-cell niche homeostasis / imaginal disc growth / open tracheal system development / positive regulation of neuron remodeling / germ-line stem cell division / negative regulation of circadian sleep/wake cycle, sleep / follicle cell of egg chamber development / lymph gland development / positive regulation of border follicle cell migration / female germ-line stem cell asymmetric division / positive regulation of fat cell proliferation / intestinal stem cell homeostasis / growth cone membrane / positive regulation of organ growth / female gonad development / 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 / insulin binding / triglyceride homeostasis / negative regulation of feeding behavior / negative regulation of macroautophagy / positive regulation of wound healing / positive regulation of neuroblast proliferation / lipid homeostasis / insulin receptor substrate binding / regulation of multicellular organism growth / developmental growth / positive regulation of cell size / phosphatidylinositol 3-kinase binding / positive regulation of TORC1 signaling / axon guidance / cholesterol homeostasis / cellular response to starvation / determination of adult lifespan / insulin receptor binding / response to cocaine / locomotory behavior / receptor protein-tyrosine kinase / circadian rhythm / hormone activity / SH3 domain binding / multicellular organism growth / insulin receptor signaling pathway / glucose homeostasis / nervous system development / regulation of cell population proliferation / protein autophosphorylation / positive regulation of cell growth / response to oxidative stress / protein tyrosine kinase activity / protein phosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / axon / positive regulation of cell population proliferation / extracellular space / 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 / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / : / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsBai, X.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structural basis of the activation of the Drosophila insulin receptor by three Drosophila insulin-like peptides
Authors: Bai, X.C.
History
DepositionNov 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: DILP1 B-chain
D: DILP1 A-chain
E: DILP1 B-chain
F: DILP1 A-chain
A: Insulin-like receptor
B: Insulin-like receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)498,45623
Polymers494,6956
Non-polymers3,76117
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide DILP1 B-chain / dILP1 / Insulin-related peptide 1


Mass: 4243.928 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VT50
#2: Protein/peptide DILP1 A-chain


Mass: 3025.562 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VT50
#3: Protein Insulin-like receptor / dIR / dInr / Insulin receptor homolog / dIRH / Receptor protein-tyrosine kinase InR


Mass: 240078.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: InR, Dir-a, Inr-a, IR, CG18402 / Production host: Baculovirus expression vector pFastBac1-HM
References: UniProt: P09208, receptor protein-tyrosine kinase
#4: 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 melanogaster insulin receptor in complex with two DILP1, symmetric conformation
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Baculovirus expression vector pFastBac1-HM
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: 2200 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
1RELIONparticle selection
2SerialEM4.1image acquisition
7Cootmodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25580 / Symmetry type: POINT
RefinementHighest resolution: 3.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314793
ELECTRON MICROSCOPYf_angle_d0.55620030
ELECTRON MICROSCOPYf_dihedral_angle_d6.4572062
ELECTRON MICROSCOPYf_chiral_restr0.0452270
ELECTRON MICROSCOPYf_plane_restr0.0042586

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