8YWQ

Crystal structure of the Fab fragment of the anti-IL-6 antibody I9H in complex with a domain-swapped IL-6 dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 
    0.277 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.243 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of signaling complex inhibition by IL-6 domain-swapped dimers.

Yudenko, A.Bukhdruker, S.Shishkin, P.Rodin, S.Burtseva, A.Petrov, A.Pigareva, N.Sokolov, A.Zinovev, E.Eliseev, I.Remeeva, A.Marin, E.Mishin, A.Gordeliy, V.Gushchin, I.Ischenko, A.Borshchevskiy, V.

(2025) Structure 33: 171-180.e5

  • DOI: https://doi.org/10.1016/j.str.2024.10.028
  • Primary Citation of Related Structures:  
    8YWP, 8YWQ, 8YWR

  • PubMed Abstract: 

    Interleukin-6 (IL-6) is a multifaceted cytokine essential in many immune system processes and their regulation. It also plays a key role in hematopoiesis, and in triggering the acute phase reaction. IL-6 overproduction is critical in chronic inflammation associated with autoimmune diseases like rheumatoid arthritis and contributes to cytokine storms in COVID-19 patients. Over 20 years ago, researchers proposed that IL-6, which is typically monomeric, can also form dimers via a domain-swap mechanism, with indirect evidence supporting their existence. The physiological significance of IL-6 dimers was shown in B-cell chronic lymphocytic leukemia. However, no structures have been reported so far. Here, we present the crystal structure of an IL-6 domain-swapped dimer that computational approaches could not predict. The structure explains why the IL-6 dimer is antagonistic to the IL-6 monomer in signaling complex formation and provides insights for IL-6 targeted therapies.


  • Organizational Affiliation

    Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of the Fab fragment of anti-IL-6 antibody I9HA [auth H]231Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of the Fab fragment of anti-IL-6 antibody I9HB [auth L]214Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-6C [auth A]185Homo sapiensMutation(s): 0 
Gene Names: IL6IFNB2
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free:  0.277 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.243 (Depositor) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.621α = 90
b = 151.875β = 90
c = 76.053γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
STARANISOdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education and Science of the Russian FederationRussian Federation075-15-2021-1354

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-12-04
    Changes: Database references
  • Version 1.2: 2025-01-15
    Changes: Database references