7NXZ

Synthetic glycoform of Human Interleukin 6

  • Classification: CYTOKINE
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2021-03-19 Released: 2021-04-07 
  • Deposition Author(s): Weyand, M., Unverzagt, C.
  • Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.206 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Natural Glycoforms of Human Interleukin 6 Show Atypical Plasma Clearance.

Reif, A.Lam, K.Weidler, S.Lott, M.Boos, I.Lokau, J.Bretscher, C.Monnich, M.Perkams, L.Schmalzlein, M.Graf, C.Fischer, J.P.Lechner, C.Hallstein, K.Becker, S.Weyand, M.Steegborn, C.Schultheiss, G.Rose-John, S.Garbers, C.Unverzagt, C.

(2021) Angew Chem Int Ed Engl 60: 13380-13387

  • DOI: https://doi.org/10.1002/anie.202101496
  • Primary Citation of Related Structures:  
    7NXZ

  • PubMed Abstract: 

    A library of glycoforms of human interleukin 6 (IL-6) comprising complex and mannosidic N-glycans was generated by semisynthesis. The three segments were connected by sequential native chemical ligation followed by two-step refolding. The central glycopeptide segments were assembled by pseudoproline-assisted Lansbury aspartylation and subsequent enzymatic elongation of complex N-glycans. Nine IL-6 glycoforms were synthesized, seven of which were evaluated for in vivo plasma clearance in rats and compared to non-glycosylated recombinant IL-6 from E. coli. Each IL-6 glycoform was tested in three animals and reproducibly showed individual serum clearances depending on the structure of the N-glycan. The clearance rates were atypical, since the 2,6-sialylated glycoforms of IL-6 cleared faster than the corresponding asialo IL-6 with terminal galactoses. Compared to non-glycosylated IL-6 the plasma clearance of IL-6 glycoforms was delayed in the presence of larger and multibranched N-glycans in most cases.


  • Organizational Affiliation

    Bioorganic Chemistry, University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-6A [auth AAA]183Homo 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
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
NLE
Query on NLE
A [auth AAA]L-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.206 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.1α = 90
b = 129.02β = 90
c = 50.1γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyDFG UN63/5-1 + SPPP1368

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary