1P9M

Crystal structure of the hexameric human IL-6/IL-6 alpha receptor/gp130 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.282 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Hexameric Structure and Assembly of the Interleukin-6/IL-6 alpha-Receptor/gp130 Complex

Boulanger, M.J.Chow, D.C.Brevnova, E.E.Garcia, K.C.

(2003) Science 300: 2101-2104

  • DOI: https://doi.org/10.1126/science.1083901
  • Primary Citation of Related Structures:  
    1P9M

  • PubMed Abstract: 

    Interleukin-6 (IL-6) is an immunoregulatory cytokine that activates a cell-surface signaling assembly composed of IL-6, the IL-6 alpha-receptor (IL-6Ralpha), and the shared signaling receptor gp130. The 3.65 angstrom-resolution structure of the extracellular signaling complex reveals a hexameric, interlocking assembly mediated by a total of 10 symmetry-related, thermodynamically coupled interfaces. Assembly of the hexameric complex occurs sequentially: IL-6 is first engaged by IL-6Ralpha and then presented to gp130in the proper geometry to facilitate a cooperative transition into the high-affinity, signaling-competent hexamer. The quaternary structures of other IL-6/IL-12 family signaling complexes are likely constructed by means of a similar topological blueprint.


  • Organizational Affiliation

    Department of Microbiology and Immunology and Department of Structural Biology, Stanford University School of Medicine, Fairchild D319, 299 Campus Drive, Stanford, CA 94305-5124, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-6 receptor beta chain299Homo sapiensMutation(s): 0 
Gene Names: IL6ST
UniProt & NIH Common Fund Data Resources
Find proteins for P40189 (Homo sapiens)
Explore P40189 
Go to UniProtKB:  P40189
PHAROS:  P40189
GTEx:  ENSG00000134352 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40189
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-6186Homo sapiensMutation(s): 0 
Gene Names: IL6 OR IFNB2
UniProt & NIH Common Fund Data Resources
Find proteins for P05231 (Homo sapiens)
Explore P05231 
Go to UniProtKB:  P05231
PHAROS:  P05231
GTEx:  ENSG00000136244 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05231
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-6 receptor alpha chain201Homo sapiensMutation(s): 0 
Gene Names: IL6R
UniProt & NIH Common Fund Data Resources
Find proteins for P08887 (Homo sapiens)
Explore P08887 
Go to UniProtKB:  P08887
PHAROS:  P08887
GTEx:  ENSG00000160712 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08887
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.282 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 279.8α = 90
b = 279.8β = 90
c = 96.7γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Refinement description