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⇱ RCSB PDB - 1ITB: TYPE-1 INTERLEUKIN-1 RECEPTOR COMPLEXED WITH INTERLEUKIN-1 BETA


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Structures from the PDB archive
1,068,577
Computed Structure Models (CSM)

 1ITB | pdb_00001itb

TYPE-1 INTERLEUKIN-1 RECEPTOR COMPLEXED WITH INTERLEUKIN-1 BETA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.325 (Depositor), 0.310 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

wwPDB Validation  3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the type-I interleukin-1 receptor complexed with interleukin-1beta.

Vigers, G.P.Anderson, L.J.Caffes, P.Brandhuber, B.J.

(1997) Nature 386: 190-194

  • PubMed9062193 Search on PubMed
  • DOI: https://doi.org/10.1038/386190a0
  • Primary Citation Related Structures: 
    1ITB

  • PubMed Abstract: 

    Interleukin-1 (IL-1) is an important mediator of inflammatory disease. The IL-1 family currently consists of two agonists, IL-1alpha and IL-1beta, and one antagonist, IL-1ra. Each of these molecules binds to the type I IL-1 receptor (IL1R). The binding of IL-1alpha or IL-1beta to IL1R is an early step in IL-1 signal transduction and blocking this interaction may therefore be a useful target for the development of new drugs. Here we report the three-dimensional structure of IL-1beta bound to the extracellular domain of IL1R (s-IL1R) at 2.5 A resolution. IL-1beta binds to s-IL1R with a 1:1 stoichiometry. The crystal structure shows that s-IL1R consists of three immunoglobulin-like domains which wrap around IL-1beta in a manner distinct from the structures of previously described cytokine-receptor complexes. The two receptor-binding regions on IL-1beta identified by site-directed mutagenesis both contact the receptor: one binds to the first two domains of the receptor, while the other binds exclusively to the third domain.


  • Organizational Affiliation
    • Amgen Inc., Boulder, Colorado 80301, USA.

Macromolecule Content 

  • Total Structure Weight: 53.62 kDa 
  • Atom Count: 3,751 
  • Modeled Residue Count: 463 
  • Deposited Residue Count: 468 
  • Unique protein chains: 2

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
INTERLEUKIN-1 BETA153Homo sapiensMutation(s): 0 
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UniProt & NIH Common Fund Data Resources
Find proteins for P01584 (Homo sapiens)
Explore P01584 
Go to UniProtKB:  P01584
PHAROS:  P01584
GTEx:  ENSG00000125538 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01584
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TYPE 1 INTERLEUKIN-1 RECEPTOR315Homo sapiensMutation(s): 0 
EC: 3.2.2.6
👁 Image
UniProt & NIH Common Fund Data Resources
Find proteins for P14778 (Homo sapiens)
Explore P14778 
Go to UniProtKB:  P14778
PHAROS:  P14778
GTEx:  ENSG00000115594 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14778
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.325 (Depositor), 0.310 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.952α = 90
b = 68.452β = 108.95
c = 65.867γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-02-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.