1ALU | pdb_00001alu

HUMAN INTERLEUKIN-6

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.277 (Depositor) 
  • R-Value Work: 
    0.213 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1ALU

This is version 1.3 of the entry. See complete history. 

Literature

1.9 A crystal structure of interleukin 6: implications for a novel mode of receptor dimerization and signaling.

Somers, W., Stahl, M., Seehra, J.S.

(1997) EMBO J 16: 989-997

  • DOI: https://doi.org/10.1093/emboj/16.5.989
  • Primary Citation Related Structures: 
    1ALU

  • PubMed Abstract: 

    Interleukin 6 (IL-6) has many biological activities in vivo, and deregulation has been implicated in many disease processes. IL-6, a 185 amino acid polypeptide was refolded, purified and crystallized. The crystals diffracted to beyond 1.9 A and the structure was solved using single isomorphous replacement. The X-ray structure of IL-6 is composed of a four helix bundle linked by loops and an additional mini-helix. 157 out of 185 residues are well defined in the final structure, with 18 N-terminal and 8 A-B loop amino acids displaying no interpretable electron density. The three-dimensional structure has been used to construct a model of IL-6 interacting with the IL-6 receptor (alpha-chain) and gp130 (beta-chain) that gives new insight into the process of molecular recognition and signaling. Based on this model, we predict a fourth binding site on IL-6, a low affinity IL-6-IL-6 interaction, which may be necessary for the sequential assembly of a functional hexameric IL-6 receptor complex.

    • Organizational Affiliation: 
    • Small Molecule Drug Discovery, Genetics Institute, Inc., Cambridge, MA 02140, USA.

Macromolecule Content 

  • Total Structure Weight: 21.67 kDa 
  • Atom Count: 1,413 
  • Modeled Residue Count: 157 
  • Deposited Residue Count: 186 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
INTERLEUKIN-6186Homo sapiensMutation(s): 0 
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.277 (Depositor) 
  • R-Value Work:  0.213 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.678α = 90
b = 49.678β = 90
c = 121.995γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
ROTAVATAdata reduction
Agrovatadata reduction
MLPHAREphasing
REFMACrefinement
CCP4data scaling
ROTAVATAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-06-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary