4DEP Immune System date Jan 21, 2012
title Structure Of The Il-1b Signaling Complex
authors C.Thomas, K.C.Garcia
compound source
Molecule: Interleukin-1 Beta
Chain: A, D
Fragment: Unp Residues 117-269
Synonym: Il-1 Beta, Catabolin
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Il-1b, Il1b, Il1f2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pgex-6p-1

Molecule: Interleukin-1 Receptor Type 1
Chain: B, E
Fragment: Unp Residues 18-336
Synonym: Il-1r-1, Il-1rt-1, Il-1rt1, Cd121 Antigen-Like Fam A, Interleukin-1 Receptor Alpha, Il-1r-Alpha, Interleukin-1 Type I, P80;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Il-1ri, Il1r, Il1r1, Il1ra, Il1rt1
Expression_system: Homo Sapiens
Expression_system_taxid: 9606

Molecule: Interleukin-1 Receptor Accessory Protein
Chain: C, F
Fragment: Unp Residues 21-367
Synonym: Il-1 Receptor Accessory Protein, Il-1racp, Interle Receptor 3, Il-1r-3, Il-1r3;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: C3orf13, Il-1racp, Il1r3, Il1rap
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.210 R_Free 0.277
length a length b length c angle alpha angle beta angle gamma
105.990 65.900 163.400 90.00 90.35 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand NAG enzyme
A, D

E, B

F, C

Primary referenceStructure of the activating IL-1 receptor signaling complex., Thomas C, Bazan JF, Garcia KC, Nat Struct Mol Biol. 2012 Mar 18;19(4):455-7. doi: 10.1038/nsmb.2260. PMID:22426547
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (242 Kb) [Save to disk]
  • Biological Unit Coordinates (4dep.pdb1.gz) 116 Kb
  • Biological Unit Coordinates (4dep.pdb2.gz) 122 Kb
  • LPC: Ligand-Protein Contacts for 4DEP
  • CSU: Contacts of Structural Units for 4DEP
  • Structure Factors (336 Kb)
  • Retrieve 4DEP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DEP from S2C, [Save to disk]
  • Re-refined 4dep structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DEP in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4DEP
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4DEP, from MSDmotif at EBI
  • Fold representative 4dep from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dep] [4dep_C] [4dep_F] [4dep_B] [4dep_E] [4dep_A] [4dep_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4DEP: [IG] [IG_like] [IL1 ] by SMART
  • Other resources with information on 4DEP
  • Community annotation for 4DEP at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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