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9ef5

Cryo-EM structure of Drosophila melanogaster insulin receptor (dmIR) bound with one DILP2, asymmetric conformation

Method: ELECTRON MICROSCOPY Dmax: 174.8 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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–2144 Chain B； UniProt 1–2144 Not recorded DILP2 B-chain × 1 （Q9VT51） DILP2 A-chain × 1 （Q9VT51） 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

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 9EF5 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 oligomeric state 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 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
9EF9 Cryo-EM structure of Drosophila melanogaster insulin receptor (dmIR) bound with three DILP5, asymmetric conformation Deposited 2024-11-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–2144（2144 aa）
Chain B 1–2144（2144 aa）
Not recorded 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
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 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

DILP2 B-chain

OrganismNot specified

UniProt Q9VT51

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 27–50 Chain D； UniProt 112–137 Not recorded Insulin-like receptor × 2 （P09208） 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

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 9EF5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9HKT Drosophila melanogaster insulin receptor ectodomain in complex with one DILP2 molecule Deposited 2024-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 112–137（26 aa）
Chain H 27–50（24 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 112–137（26 aa）
Chain F 27–50（24 aa）
Chain G 112–137（26 aa）
Chain H 27–50（24 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

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INSL2_DROME
Isoform —
PDB entities 2, 3
Chains and sequence ranges Author chain C； PDBConstruct 1–24； UniProt 27–50 Author chain D； PDBConstruct 1–26； UniProt 112–137

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 9ef5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9ef5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9ef5
Deposition date deposition_date2024-11-19
Structure title titleCryo-EM structure of Drosophila melanogaster insulin receptor (dmIR) bound with one DILP2, 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_guinier49.60 Å
Radius of gyration Rg (electron density) rg_electron50.16 Å
Forward intensity I(0) i0400949000.00
Molecular weight molecular_weight163910.0 kDa
Excluded volume excluded_volume204580 ų
Envelope volume envelope_volume319070 ų
Hydration-shell volume shell_volume55933 ų
Envelope diameter envelope_diameter171.9 Å
Shell Rg shell_rg51.23 Å
Envelope Rg envelope_rg48.26 Å
Shape Rg shape_rg50.17 Å
Total Rg total_rg50.19 Å
Total atoms total_atoms22796
Residues n_residues1421
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 dmax174.8 Å
Rg (real space) rg_real50.05 Å
Rg uncertainty (real space) rg_real_error2.22 Å
I(0) (real space) i0_real4.0090e+08
I(0) uncertainty (real space) i0_real_error8.8630e+06
Rg (reciprocal space) rg_reciprocal49.60 Å
I(0) (reciprocal space) i0_reciprocal400700000.0000
Solution quality estimate total_estimate0.8536
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary169.3 Å
Skewness Skewness skewness0.428
Kurtosis Kurtosis kurtosis-0.487
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha20950000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.818; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.849; Smooth: 0.790
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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)