8oe0

Cryo-EM structure of a pre-dimerized murine IL-12 complete extracellular signaling complex (Class 2).

Method: ELECTRON MICROSCOPY Dmax: 185.2 Å Quality: GOOD

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

Interleukin-12 subunit alpha

Mus musculus

UniProt P43431

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 23–215 Not recorded Interleukin-12 subunit beta × 1 (P43432) Interleukin-12 receptor subunit beta-1,Death-associated protein kinase 1 × 1 (Q60837,P53355) Interleukin-12 receptor subunit beta-2,Calmodulin-1 × 1 (P97378,P0DP23) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;HEPES-buffered saline (HBS) with added calcium chloride: 25 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM CaCl cryo-EM vitrification conditions:Cryogen ETHANE;Leica EM GP2, 5 s. blotting time. Resolution 4.60 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 IL12A_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–193; UniProt 23–215

Interleukin-12 subunit beta

Mus musculus

UniProt P43432

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 23–335 Not recorded Interleukin-12 subunit alpha × 1 (P43431) Interleukin-12 receptor subunit beta-1,Death-associated protein kinase 1 × 1 (Q60837,P53355) Interleukin-12 receptor subunit beta-2,Calmodulin-1 × 1 (P97378,P0DP23) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;HEPES-buffered saline (HBS) with added calcium chloride: 25 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM CaCl cryo-EM vitrification conditions:Cryogen ETHANE;Leica EM GP2, 5 s. blotting time. Resolution 4.60 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.

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IL12B_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–313; UniProt 23–335

Interleukin-12 receptor subunit beta-1,Death-associated protein kinase 1

Mus musculus

UniProt P53355

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 300–319 Not recorded Interleukin-12 subunit alpha × 1 (P43431) Interleukin-12 subunit beta × 1 (P43432) Interleukin-12 receptor subunit beta-2,Calmodulin-1 × 1 (P97378,P0DP23) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;HEPES-buffered saline (HBS) with added calcium chloride: 25 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM CaCl cryo-EM vitrification conditions:Cryogen ETHANE;Leica EM GP2, 5 s. blotting time. Resolution 4.60 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.

77 other PDB entries and 81 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DAPK1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 553–572; UniProt 300–319

Interleukin-12 receptor subunit beta-1,Death-associated protein kinase 1

Mus musculus

UniProt Q60837

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 20–561 Not recorded Interleukin-12 subunit alpha × 1 (P43431) Interleukin-12 subunit beta × 1 (P43432) Interleukin-12 receptor subunit beta-2,Calmodulin-1 × 1 (P97378,P0DP23) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;HEPES-buffered saline (HBS) with added calcium chloride: 25 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM CaCl cryo-EM vitrification conditions:Cryogen ETHANE;Leica EM GP2, 5 s. blotting time. Resolution 4.60 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 I12R1_MOUSE
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–542; UniProt 20–561

Interleukin-12 receptor subunit beta-2,Calmodulin-1

Mus musculus

UniProt P0DP23

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 5–149 Not recorded Interleukin-12 subunit alpha × 1 (P43431) Interleukin-12 subunit beta × 1 (P43432) Interleukin-12 receptor subunit beta-1,Death-associated protein kinase 1 × 1 (Q60837,P53355) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;HEPES-buffered saline (HBS) with added calcium chloride: 25 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM CaCl cryo-EM vitrification conditions:Cryogen ETHANE;Leica EM GP2, 5 s. blotting time. Resolution 4.60 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.

213 other PDB entries and 279 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CALM1_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 625–769; UniProt 5–149

Interleukin-12 receptor subunit beta-2,Calmodulin-1

Mus musculus

UniProt P97378

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 24–637 Not recorded Interleukin-12 subunit alpha × 1 (P43431) Interleukin-12 subunit beta × 1 (P43432) Interleukin-12 receptor subunit beta-1,Death-associated protein kinase 1 × 1 (Q60837,P53355) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;HEPES-buffered saline (HBS) with added calcium chloride: 25 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM CaCl cryo-EM vitrification conditions:Cryogen ETHANE;Leica EM GP2, 5 s. blotting time. Resolution 4.60 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.

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

View Construct and Data Evidence
UniProt name I12R2_MOUSE
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–614; UniProt 24–637

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 8oe0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8oe0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8oe0
Deposition date deposition_date2023-03-10
Structure title titleCryo-EM structure of a pre-dimerized murine IL-12 complete extracellular signaling complex (Class 2).
Keywords keywordsComplex, Cytokine, Receptor, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier55.26
Radius of gyration Rg (electron density) rg_electron55.42
Forward intensity I(0) i0443395000.00
Molecular weight molecular_weight170660.0 kDa
Excluded volume excluded_volume212090 ų
Envelope volume envelope_volume377920 ų
Hydration-shell volume shell_volume60664 ų
Envelope diameter envelope_diameter188.2
Shell Rg shell_rg54.78
Envelope Rg envelope_rg51.81
Shape Rg shape_rg55.45
Total Rg total_rg55.27
Total atoms total_atoms11980
Residues n_residues1500
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 dmax185.2
Rg (real space) rg_real55.49
Rg uncertainty (real space) rg_real_error2.26
I(0) (real space) i0_real4.4340e+08
I(0) uncertainty (real space) i0_real_error9.6030e+06
Rg (reciprocal space) rg_reciprocal55.04
I(0) (reciprocal space) i0_reciprocal443100000.0000
Solution quality estimate total_estimate0.8601
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary59.5
Skewness Skewness skewness0.338
Kurtosis Kurtosis kurtosis-0.575
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16300000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.541

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)