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9ef9

Cryo-EM structure of Drosophila melanogaster insulin receptor (dmIR) bound with three DILP5, asymmetric conformation

Method: ELECTRON MICROSCOPY Dmax: 172.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Insulin-like receptor

Drosophila melanogaster

UniProt P09208

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1–2144 Chain B； UniProt 1–2144 Not recorded DILP5 A-chain × 3 （Q7KUD5） DILP5 B-chain × 3 （Q7KUD5） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9EF9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8CLS Drosophila melanogaster insulin receptor ectodomain in complex with DILP5 Deposited 2023-02-17 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 264–1310（1047 aa）
Chain B 264–1310（1047 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9EF1 Cryo-EM structure of Drosophila melanogaster insulin receptor (dmIR) bound with one DILP1, asymmetric conformation Deposited 2024-11-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–2144（2144 aa）
Chain B 1–2144（2144 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
9EF4 Cryo-EM structure of Drosophila melanogaster insulin receptor (dmIR) bound with two DILP1, symmetric conformation Deposited 2024-11-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–2144（2144 aa）
Chain B 1–2144（2144 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9EF5 Cryo-EM structure of Drosophila melanogaster insulin receptor (dmIR) bound with one DILP2, asymmetric conformation Deposited 2024-11-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–2144（2144 aa）
Chain B 1–2144（2144 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9HKT Drosophila melanogaster insulin receptor ectodomain in complex with one DILP2 molecule Deposited 2024-12-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 264–1310（1047 aa）
Chain B 264–1310（1047 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Hepes pH 7.5, 200mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9HNI Drosophila melanogaster insulin receptor ectodomain in complex with two DILP2 molecules Deposited 2024-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 264–1310（1047 aa）
Chain B 264–1310（1047 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Hepes pH 7.5, 200mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.25 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INSR_DROME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–2144； UniProt 1–2144 Author chain B； PDBConstruct 1–2144； UniProt 1–2144

DILP5 A-chain

OrganismNot specified

UniProt Q7KUD5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain C； UniProt 84–108 Chain D； UniProt 24–51 Chain E； UniProt 84–108 Chain F； UniProt 24–51 Chain G； UniProt 84–108 Chain H； UniProt 24–51 Not recorded Insulin-like receptor × 2 （P09208） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9EF9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2WFU Crystal structure of DILP5 variant DB Deposited 2009-04-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 87–108（22 aa） Fragment：RESIDUES 87-108
Chain B 24–47（24 aa） Fragment：RESIDUES 24-47
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 20% PEG4000
Resolution 1.85 Å R-free 0.256
2WFV Crystal structure of DILP5 variant C4 Deposited 2009-04-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 84–108（25 aa） Fragment：RESIDUES 84-108
Chain B 24–46（23 aa） Fragment：RESIDUES 24-46
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 20% PEG4000
Resolution 1.85 Å R-free 0.232
6FEY Crystal structure of Drosophila neural ectodermal development factor Imp-L2 with Drosophila DILP5 insulin Deposited 2018-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain G 84–108（25 aa）
Chain H 24–51（28 aa）
Chain I 84–108（25 aa）
Chain J 24–51（28 aa）
Mutation：K95N Mutation：K95N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；Cp 10 mg/ml, 8-10% w/v PEG 4k or 6K, 20 mM MgCl2, 0.1 M HEPES pH 6.8-7.5
Resolution 3.48 Å R-free 0.345
6FEY Crystal structure of Drosophila neural ectodermal development factor Imp-L2 with Drosophila DILP5 insulin Deposited 2018-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 84–108（25 aa）
Chain F 24–51（28 aa）
Chain K 84–108（25 aa）
Chain L 24–51（28 aa）
Mutation：K95N Mutation：K95N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；Cp 10 mg/ml, 8-10% w/v PEG 4k or 6K, 20 mM MgCl2, 0.1 M HEPES pH 6.8-7.5
Resolution 3.48 Å R-free 0.345
8CLS Drosophila melanogaster insulin receptor ectodomain in complex with DILP5 Deposited 2023-02-17 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 84–108（25 aa）
Chain D 24–51（28 aa）
Chain E 84–108（25 aa）
Chain F 24–51（28 aa）
Chain G 84–108（25 aa）
Chain H 24–51（28 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INSL5_DROME
Isoform —
PDB entities 2, 3
Chains and sequence ranges Author chain C； PDBConstruct 1–25； UniProt 84–108 Author chain E； PDBConstruct 1–25； UniProt 84–108 Author chain G； PDBConstruct 1–25； UniProt 84–108 Author chain D； PDBConstruct 1–28； UniProt 24–51 Author chain F； PDBConstruct 1–28； UniProt 24–51 Author chain H； PDBConstruct 1–28； UniProt 24–51

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9ef9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9ef9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9ef9
Deposition date deposition_date2024-11-19
Structure title titleCryo-EM structure of Drosophila melanogaster insulin receptor (dmIR) bound with three DILP5, asymmetric conformation
Keywords keywordsInsulin receptor, DILP, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier51.37 Å
Radius of gyration Rg (electron density) rg_electron51.35 Å
Forward intensity I(0) i0684685000.00
Molecular weight molecular_weight212130.0 kDa
Excluded volume excluded_volume263560 ų
Envelope volume envelope_volume409000 ų
Hydration-shell volume shell_volume69098 ų
Envelope diameter envelope_diameter174.7 Å
Shell Rg shell_rg52.73 Å
Envelope Rg envelope_rg49.55 Å
Shape Rg shape_rg51.33 Å
Total Rg total_rg51.46 Å
Total atoms total_atoms29322
Residues n_residues1851
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax172.2 Å
Rg (real space) rg_real51.37 Å
Rg uncertainty (real space) rg_real_error1.67 Å
I(0) (real space) i0_real6.8470e+08
I(0) uncertainty (real space) i0_real_error1.3700e+07
Rg (reciprocal space) rg_reciprocal51.36 Å
I(0) (reciprocal space) i0_reciprocal684700000.0000
Solution quality estimate total_estimate0.8274
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary61.1 Å
Skewness Skewness skewness0.228
Kurtosis Kurtosis kurtosis-0.582
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha33850000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)