7NXZ | pdb_00007nxz

Synthetic glycoform of Human Interleukin 6

• PDB DOI: https://doi.org/10.2210/pdb7NXZ/pdb

• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.253 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.206 (DCC) 

Starting Model: experimental

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

• PubMed: 33756033 
• DOI: https://doi.org/10.1002/anie.202101496
• Primary Citation 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.

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Organizational Affiliation: 
• Bioorganic Chemistry, University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany.
Department of Pathology, Medical Faculty, Otto von Guericke University Magdeburg, 39120, Magdeburg, Germany.
Department of Biochemistry, Kiel University, 24098, Kiel, Germany.
Protein Engineering & Antibody Technologies, Merck Healthcare KGaA, Frankfurter Str. 250, 64293, Darmstadt, Germany.
Department of Biochemistry, University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany.
Animal Welfare, Kiel University, 24098, Kiel, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 20.82 kDa 
• Atom Count: 1,327 
• Modeled Residue Count: 159 
• Deposited Residue Count: 183 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-6	A [auth AAA]	183	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P05231 (Homo sapiens) Explore P05231  Go to UniProtKB:  P05231
PHAROS:  P05231 GTEx:  ENSG00000136244

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NLE	A [auth AAA]	L-PEPTIDE LINKING	C6 H13 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.253 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.206 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.1	α = 90
b = 129.02	β = 90
c = 50.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-04-07 
Deposition Author(s): Weyand, M., Unverzagt, C.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	DFG UN63/5-1 + SPPP1368

Revision History  

• 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