4DEP

Structure of the IL-1b signaling complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the activating IL-1 receptor signaling complex.

Thomas, C.Bazan, J.F.Garcia, K.C.

(2012) Nat.Struct.Mol.Biol. 19: 455-457

  • DOI: 10.1038/nsmb.2260

  • PubMed Abstract: 
  • Interleukin-1 (IL-1)-family cytokines are mediators of innate and adaptive immunity. They exert proinflammatory effects by binding a primary receptor that recruits a receptor accessory protein to form a signaling-competent heterotrimeric complex. Her ...

    Interleukin-1 (IL-1)-family cytokines are mediators of innate and adaptive immunity. They exert proinflammatory effects by binding a primary receptor that recruits a receptor accessory protein to form a signaling-competent heterotrimeric complex. Here we present the crystal structure of IL-1β bound to its primary receptor IL-1RI and its receptor accessory protein IL-1RAcP, providing insight into how IL-1-type cytokines initiate signaling and revealing an evolutionary relationship with the fibroblast growth factor receptor family.


    Organizational Affiliation

    Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interleukin-1 beta
A, D
158Homo sapiensMutation(s): 0 
Gene Names: IL1B (IL1F2)
Find proteins for P01584 (Homo sapiens)
Go to Gene View: IL1B
Go to UniProtKB:  P01584
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Interleukin-1 receptor type 1
B, E
321Homo sapiensMutation(s): 0 
Gene Names: IL1R1 (IL1R, IL1RA, IL1RT1)
Find proteins for P14778 (Homo sapiens)
Go to Gene View: IL1R1
Go to UniProtKB:  P14778
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Interleukin-1 receptor accessory protein
C, F
349Homo sapiensMutation(s): 0 
Gene Names: IL1RAP (C3orf13, IL1R3)
Find proteins for Q9NPH3 (Homo sapiens)
Go to Gene View: IL1RAP
Go to UniProtKB:  Q9NPH3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
B, C, E, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 105.990α = 90.00
b = 65.900β = 90.35
c = 163.400γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Blu-Icedata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-04-18
    Type: Database references