8YWQ | pdb_00008ywq

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

• PDB DOI: https://doi.org/10.2210/pdb8YWQ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus, Homo sapiens
• Mutation(s): No 


• Deposited: 2024-03-31 Released: 2024-11-06 
• Deposition Author(s): Bukhdruker, S., Yudenko, A., Marin, E., Remeeva, A., Rodin, S., Burtseva, A., Petrov, A., Ischenko, A., Borshchevskiy, V.
• Funding Organization(s): Ministry of Education and Science of the Russian Federation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.277 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Models: experimental

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

• PubMed: 39566503 
• DOI: https://doi.org/10.1016/j.str.2024.10.028
• Primary Citation 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.

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Organizational Affiliation: 
• Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia.
Institute of Experimental Medicine, St. Petersburg 197022, Russia; Research Institute of Highly Pure Biopreparations, St. Petersburg 197110, Russia.
St. Petersburg Pasteur Institute, St. Petersburg 197101, Russia; Research Institute of Highly Pure Biopreparations, St. Petersburg 197110, Russia.
Research Institute of Highly Pure Biopreparations, St. Petersburg 197110, Russia; Medicinal Chemistry Center, Togliatti State University, Togliatti, Samara Region 445020, Russia.
Institute of Experimental Medicine, St. Petersburg 197022, Russia.
Alferov University, St. Petersburg 194021, Russia; St. Petersburg School of Physics, Mathematics, and Computer Science, HSE University, St. Petersburg 194100, Russia.
Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France.
St. Petersburg Pasteur Institute, St. Petersburg 197101, Russia; Research Institute of Highly Pure Biopreparations, St. Petersburg 197110, Russia. Electronic address: [e-mail].
Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia; Joint Institute for Nuclear Research, Dubna, Moscow Region 141980, Russia. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 69.34 kDa 
• Atom Count: 4,270 
• Modeled Residue Count: 579 
• Deposited Residue Count: 630 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of the Fab fragment of anti-IL-6 antibody I9H	A [auth H]	231	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of the Fab fragment of anti-IL-6 antibody I9H	B [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-6	C [auth A]	185	Homo sapiens	Mutation(s): 0  Gene Names: IL6, IFNB2
UniProt & NIH Common Fund Data Resources
Find proteins for P05231 (Homo sapiens) Explore P05231  Go to UniProtKB:  P05231
PHAROS:  P05231 GTEx:  ENSG00000136244

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	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), 0.272 (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 = 126.621	α = 90
b = 151.875	β = 90
c = 76.053	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
STARANISO	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Bukhdruker, S., Yudenko, A., Marin, E., Remeeva, A., Rodin, S., Burtseva, A., Petrov, A., Ischenko, A., Borshchevskiy, V.

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Funding Organization	Location	Grant Number
Ministry of Education and Science of the Russian Federation	Russian Federation	075-15-2021-1354

Revision History  

• 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