7yq3

human insulin receptor bound with A43 DNA aptamer and insulin

Method: ELECTRON MICROSCOPY Dmax: 170.3 Å Quality: REASONABLE

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

Insulin A chain

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–DNA Heteromer Protein × 4 DNA 1 PDB declaration: pentameric(5) Consistent with all polymer counts Chain A; UniProt 90–110 Not recorded Insulin, isoform 2 × 1 (F8WCM5) Isoform Short of Insulin receptor × 2 (P06213) IR-A43 aptamer × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 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.

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 1
Chains and sequence ranges Author chain A; PDBConstruct 1–21; UniProt 90–110

Insulin, isoform 2

Homo sapiens

UniProt F8WCM5

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–DNA Heteromer Protein × 4 DNA 1 PDB declaration: pentameric(5) Consistent with all polymer counts Chain B; UniProt 27–51 Not recorded Insulin A chain × 1 (P01308) Isoform Short of Insulin receptor × 2 (P06213) IR-A43 aptamer × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INSR2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–25; UniProt 27–51

Isoform Short of Insulin receptor

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–DNA Heteromer Protein × 4 DNA 1 PDB declaration: pentameric(5) Consistent with all polymer counts Chain E; UniProt 28–934 Chain F; UniProt 28–934 Not recorded Insulin A chain × 1 (P01308) Insulin, isoform 2 × 1 (F8WCM5) IR-A43 aptamer × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 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.

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 3
Chains and sequence ranges Author chain E; PDBConstruct 1–907; UniProt 28–934 Author chain F; PDBConstruct 1–907; UniProt 28–934

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 7yq3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7yq3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7yq3
Deposition date deposition_date2022-08-05
Structure title titlehuman insulin receptor bound with A43 DNA aptamer and insulin
Keywords keywordsreceptor-ligand complex, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier49.59
Radius of gyration Rg (electron density) rg_electron49.65
Forward intensity I(0) i0667970000.00
Molecular weight molecular_weight205380.0 kDa
Excluded volume excluded_volume253340 ų
Envelope volume envelope_volume402620 ų
Hydration-shell volume shell_volume69776 ų
Envelope diameter envelope_diameter180.9
Shell Rg shell_rg51.75
Envelope Rg envelope_rg48.31
Shape Rg shape_rg49.65
Total Rg total_rg49.76
Total atoms total_atoms14393
Residues n_residues1729
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 dmax170.3
Rg (real space) rg_real51.98
Rg uncertainty (real space) rg_real_error0.76
I(0) (real space) i0_real6.6890e+08
I(0) uncertainty (real space) i0_real_error1.1860e+07
Rg (reciprocal space) rg_reciprocal49.60
I(0) (reciprocal space) i0_reciprocal667800000.0000
Solution quality estimate total_estimate0.6690
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.9
Skewness Skewness skewness0.467
Kurtosis Kurtosis kurtosis-0.332
Angular range angular_range— – 0.1600 −1
Current regularization parameter α current_alpha1.3960
Highest regularization parameter α highest_alpha53040000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.892; Stabil: 0.871; Sysdev: 0.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.493

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id7yq3E01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
Homologous superfamily homologous superfamily10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2
Domain ID domain_id7yq3E02
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology20 — 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
Homologous superfamily homologous superfamily20 — Receptor L-domain
Domain ID domain_id7yq3F01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
Homologous superfamily homologous superfamily10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2
Domain ID domain_id7yq3F02
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology20 — 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
Homologous superfamily homologous superfamily20 — Receptor L-domain
Domain ID domain_id7yq3F03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)