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4dep

Structure of the IL-1b signaling complex

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Interleukin-1 beta

Homo sapiens

UniProt P01584

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Interleukin-1 receptor type 1 × 1 （P14778） Interleukin-1 receptor accessory protein × 1 （Q9NPH3） 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 water × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Interleukin-1 receptor type 1 × 1 （P14778） Interleukin-1 receptor accessory protein × 1 （Q9NPH3） 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1hib 1i1b 1iob 1l2h 1s0l 1t4q 1too 1tp0 1twe 1twm 21bi 2i1b

54 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1itb 2kh2 3o4o 4dep 4dep 4g6j 4g6m 5bvp 7chy 7chz 7z4t 8ryk

13 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name IL1B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–158； UniProt 117–269 Author chain D； PDBConstruct 6–158； UniProt 117–269

Interleukin-1 receptor type 1

Homo sapiens

UniProt P14778

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Interleukin-1 beta × 1 （P01584） Interleukin-1 receptor accessory protein × 1 （Q9NPH3） 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 water × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Interleukin-1 beta × 1 （P01584） Interleukin-1 receptor accessory protein × 1 （Q9NPH3） 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1g0y 1ira 1itb 4dep 4dep 4gaf

6 assemblies

View Construct and Data Evidence
UniProt name IL1R1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 3–321； UniProt 18–336 Author chain E； PDBConstruct 3–321； UniProt 18–336

Interleukin-1 receptor accessory protein

Homo sapiens

UniProt Q9NPH3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Interleukin-1 beta × 1 （P01584） Interleukin-1 receptor type 1 × 1 （P14778） 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 water × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Interleukin-1 beta × 1 （P01584） Interleukin-1 receptor type 1 × 1 （P14778） 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
7fcc

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3o4o 4dep 4dep

3 assemblies

View Construct and Data Evidence
UniProt name IL1AP_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 3–349； UniProt 21–367 Author chain F； PDBConstruct 3–349； UniProt 21–367

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id4dep
Deposition date deposition_date2012-01-21
Structure title titleStructure of the IL-1b signaling complex
Keywords keywordsb-trefoil, immunoglobulin, immune system, extracellular; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4dep__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4dep__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4dep__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）32.16 Å
Rg (electron density)31.57 Å
Total Rg31.98 Å
Atom count5689
Residues734
Excluded volume101010 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4dep__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4dep__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

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6. Fold Classification (SCOP + CATH) 23 domains

SCOP 2.08 (9 domains)

Domain ID domain_idd4depa_
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.1 — Cytokine
Family Family familyb.42.1.2 — Interleukin-1 (IL-1)
Domain ID domain_idd4depb1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd4depb2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd4depb3
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd4depd1
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.1 — Cytokine
Family Family familyb.42.1.2 — Interleukin-1 (IL-1)
Domain ID domain_idd4depd2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4depe1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd4depe2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd4depe3
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches

CATH v4.4 (14 domains)

Domain ID domain_id4depA00
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50 —
Domain ID domain_id4depB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4depB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4depB03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4depC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4depC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4depC03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4depD00
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50 —
Domain ID domain_id4depE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4depE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4depE03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4depF01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4depF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4depF03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (1)