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- EMDB-52310: Drosophila melanogaster insulin receptor ectodomain in complex wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-52310
TitleDrosophila melanogaster insulin receptor ectodomain in complex with two DILP2 molecules
Map dataPrimary map after PostProcess in Relion
Sample
  • Complex: Drosophila insulin receptor ectodomain with DILP-2
    • Protein or peptide: Probable insulin-like peptide 2
    • Protein or peptide: Probable insulin-like peptide 2
    • Protein or peptide: Insulin-like receptor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsReceptor / Dilp2 / Drosophila / complex / SIGNALING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.25 Å
AuthorsShafi T / Moroz OV / Jenkins HT / Chechik M / Isupov MN / Brzozowski AM
Funding support United Kingdom, 1 items
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 OV / Jenkins HT / Chechik M / Isupov MN / Brzozowski AM
History
DepositionDec 10, 2024-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52310.png

Downloads & links

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Map

FileDownload / File: emd_52310.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map after PostProcess in Relion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 512 pix.
= 293.888 Å		0.57 Å/pix.
x 512 pix.
= 293.888 Å		0.57 Å/pix.
x 512 pix.
= 293.888 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.574 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0006
Minimum - Maximum-0.0010186469 - 0.003258286
Average (Standard dev.)0.00002268779 (±0.00015425308)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 293.888 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52310_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map odd

Fileemd_52310_half_map_1.map
Annotationhalf map odd
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map even

Fileemd_52310_half_map_2.map
Annotationhalf map even
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Drosophila insulin receptor ectodomain with DILP-2

EntireName: Drosophila insulin receptor ectodomain with DILP-2
Components
  • Complex: Drosophila insulin receptor ectodomain with DILP-2
    • Protein or peptide: Probable insulin-like peptide 2
    • Protein or peptide: Probable insulin-like peptide 2
    • Protein or peptide: Insulin-like receptor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Drosophila insulin receptor ectodomain with DILP-2

SupramoleculeName: Drosophila insulin receptor ectodomain with DILP-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 0.25 kDa/nm

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Macromolecule #1: Probable insulin-like peptide 2

MacromoleculeName: Probable insulin-like peptide 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 3.025617 KDa
SequenceString:
QGIVERCCKK SCDMKALREY CSVVRN

UniProtKB: Insulin-like peptide 2

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Macromolecule #2: Probable insulin-like peptide 2

MacromoleculeName: Probable insulin-like peptide 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 2.75017 KDa
SequenceString:
TLCSEKLNEV LSMVCEEYNP VIPH

UniProtKB: Insulin-like peptide 2

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Macromolecule #3: Insulin-like receptor

MacromoleculeName: Insulin-like receptor / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 117.744164 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHNYSYSPGI SLLLFILLAN TLAIQAVVLP AHQQHLLHND IADGLDKTAL SVSGTQSRWT RSESNPTMRL SQNVKPCKSM DIRNMVSHF NQLENCTVIE GFLLIDLIND ASPLNRSFPK LTEVTDYIII YRVTGLHSLS KIFPNLSVIR GNKLFDGYAL V VYSNFDLM ...String:
MHNYSYSPGI SLLLFILLAN TLAIQAVVLP AHQQHLLHND IADGLDKTAL SVSGTQSRWT RSESNPTMRL SQNVKPCKSM DIRNMVSHF NQLENCTVIE GFLLIDLIND ASPLNRSFPK LTEVTDYIII YRVTGLHSLS KIFPNLSVIR GNKLFDGYAL V VYSNFDLM DLGLHKLRSI TRGGVRIEKN HKLCYDRTID WLEILAENET QLVVLTENGK EKECRLSKCP GEIRIEEGHD TT AIEGELN ASCQLHNNRR LCWNSKLCQT KCPEKCRNNC IDEHTCCSQD CLGGCVIDKN GNESCISCRN VSFNNICMDS CPK GYYQFD SRCVTANECI TLTKFETNSV YSGIPYNGQC ITHCPTGYQK SENKRMCEPC PGGKCDKECS SGLIDSLERA REFH GCTII TGTEPLTISI KRESGAHVMD ELKYGLAAVH KIQSSLMVHL TYGLKSLKFF QSLTEISGDP PMDADKYALY VLDNR DLDE LWGPNQTVFI RKGGVFFHFN PKLCVSTINQ LLPMLASKPK FFEKSDVGAD SNGNRGSCGT AVLNVTLQSV GANSAM LNV TTKVEIGEPQ KPSNATIVFK DPRAFIGFVF YHMIDPYGNS TKSSDDPCDD RWKVSSPEKS GVMVLSNLIP YTNYSYY VR TMAISSELTN AESDVKNFRT NPGRPSKVTE VVATAISDSK INVTWSYLDK PYGVLTRYFI KAKLINRPTR NNNRDYCT E PLVKAMENDL PATTPTKKIS DPLAGDCKCV EGSKKTSSQE YDDRKVQAGM EFENALQNFI FVPNIRKSKN GSSDKSDGA EGAALDSNAI PNGGATNPSR RRRDVALEPE LDDVEGSVLL RHVRSITDDT DAFFEKDDEN TYKDEEDLSS NKQFYEVFAK ELPPNQTHF VFEKLRHFTR YAIFVVACRE EIPSEKLRDT SFKKSLCSDY DTVFQTTKRK KFADIVMDLK VDLEHANNTE S PVRVRWTP PVDPNGEIVT YEVAYKLQKP DQVEEKKCIP AADFNQTAGY LIKLNEGLYS FRVRANSIAG YGDFTEVEHI KV EPPPSYA K

UniProtKB: Insulin-like receptor

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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: 17 / 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

Concentration0.2 mg/mL
BufferpH: 7.5 / Details: 20mM Hepes pH 7.5, 200mM NaCl
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Pressure: 0.00038 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV
Detailsthe receptor ectodomain was mixed with Dilp2 in 1:40 ratio

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 59000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8cls


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9hni:
Drosophila melanogaster insulin receptor ectodomain in complex with two DILP2 molecules

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