3O4O Immune System date Jul 27, 2010
title Crystal Structure Of An Interleukin-1 Receptor Complex
authors X.Q.Wang, D.L.Wang, S.Y.Zhang, L.Li, X.Liu, K.R.Mei
compound source
Molecule: Interleukin-1 Beta
Chain: A
Synonym: Il-1beta, Il-1 Beta, Catabolin
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-1

Molecule: Interleukin-1 Receptor Type 2
Chain: C
Fragment: Il-1rii Ectodomain, Residues 14-343
Synonym: Il-1rii, Il-1rt-2, Il-1rt2, Il-1r-2, Interleukin-1 Type II, Interleukin-1 Receptor Beta, Il-1r-Beta, Cd121 Ant Family Member B, Cdw121b;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pacgp67-A

Molecule: Interleukin-1 Receptor Accessory Protein
Chain: B
Fragment: Il-1racp Ectodomain, Residues 21-350
Synonym: Il-1racp, Il-1 Receptor Accessory Protein, Interle Receptor 3, Il-1r-3, Il-1r3;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pacgp67-A
symmetry Space Group: P 21 21 21
R_factor 0.252 R_Free 0.289
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.830 177.470 180.660 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.30 Å
ligand NAG enzyme
Primary referenceStructural insights into the assembly and activation of IL-1beta with its receptors., Wang D, Zhang S, Li L, Liu X, Mei K, Wang X, Nat Immunol. 2010 Aug 29. PMID:20802483
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (291 Kb) [Save to disk]
  • Biological Unit Coordinates (3o4o.pdb1.gz) 285 Kb
  • LPC: Ligand-Protein Contacts for 3O4O
  • CSU: Contacts of Structural Units for 3O4O
  • Structure Factors (177 Kb)
  • Retrieve 3O4O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3O4O from S2C, [Save to disk]
  • Re-refined 3o4o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3O4O 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 3O4O
  • 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 3O4O, from MSDmotif at EBI
  • Fold representative 3o4o from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3o4o] [3o4o_B] [3o4o_A] [3o4o_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3O4O: [IG] [IL1 ] by SMART
  • Alignments of the sequence of 3O4O with the sequences similar proteins can be viewed for 3O4O's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3O4O
  • Community annotation for 3O4O at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science