7md4

Insulin receptor ectodomain dimer complexed with two IRPA-3 partial agonists

Method: ELECTRON MICROSCOPY Dmax: 164.6 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform Short of Insulin receptor subunit alpha

Homo sapiens

UniProt P06213

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 × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain A; UniProt 28–944 Chain B; UniProt 28–944 Chain M; UniProt 721–747 Chain N; UniProt 721–747 Fragment:C-terminal helix Fragment:extracellular domain Insulin chain A × 4 (P01308) Insulin B chain × 4 (P01308) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.50 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.

85 other PDB entries and 99 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INSR_HUMAN
Isoform P06213-2
PDB entities 1, 2
Chains and sequence ranges Author chain M; PDBConstruct 4–30; UniProt 721–747 Author chain N; PDBConstruct 4–30; UniProt 721–747 Author chain A; PDBConstruct 1–917; UniProt 28–944 Author chain B; PDBConstruct 1–917; UniProt 28–944

Insulin chain A

Homo sapiens

UniProt P01308

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 × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain O; UniProt 90–110 Chain P; UniProt 25–54 Chain Q; UniProt 90–110 Chain R; UniProt 25–54 Chain S; UniProt 90–110 Chain T; UniProt 25–54 Chain U; UniProt 90–110 Chain V; UniProt 25–54 Not recorded Isoform Short of Insulin receptor subunit alpha × 2 (P06213) Isoform Short of Insulin receptor × 2 (P06213) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.50 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.

369 other PDB entries and 583 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INS_HUMAN
Isoform
PDB entities 3, 4
Chains and sequence ranges Author chain O; PDBConstruct 1–21; UniProt 90–110 Author chain Q; PDBConstruct 1–21; UniProt 90–110 Author chain S; PDBConstruct 1–21; UniProt 90–110 Author chain U; PDBConstruct 1–21; UniProt 90–110 Author chain P; PDBConstruct 1–30; UniProt 25–54 Author chain R; PDBConstruct 1–30; UniProt 25–54 Author chain T; PDBConstruct 1–30; UniProt 25–54 Author chain V; PDBConstruct 1–30; UniProt 25–54

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 7md4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7md4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7md4
Deposition date deposition_date2021-04-03
Structure title titleInsulin receptor ectodomain dimer complexed with two IRPA-3 partial agonists
Keywords keywordsInsulin receptor, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier53.06
Radius of gyration Rg (electron density) rg_electron52.49
Forward intensity I(0) i0575276000.00
Molecular weight molecular_weight197920.0 kDa
Excluded volume excluded_volume247030 ų
Envelope volume envelope_volume412490 ų
Hydration-shell volume shell_volume67644 ų
Envelope diameter envelope_diameter164.0
Shell Rg shell_rg55.60
Envelope Rg envelope_rg49.03
Shape Rg shape_rg52.49
Total Rg total_rg52.63
Total atoms total_atoms13903
Residues n_residues1720
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax164.6
Rg (real space) rg_real52.93
Rg uncertainty (real space) rg_real_error1.65
I(0) (real space) i0_real5.7530e+08
I(0) uncertainty (real space) i0_real_error1.0550e+07
Rg (reciprocal space) rg_reciprocal53.14
I(0) (reciprocal space) i0_reciprocal575400000.0000
Solution quality estimate total_estimate0.8801
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary76.8
Skewness Skewness skewness0.042
Kurtosis Kurtosis kurtosis-0.781
Angular range angular_range— – 0.1500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25080000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.975; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.512

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)