4NI9

Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (SOMAMER SL1025), FORM 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of interleukin-6 in complex with a modified nucleic Acid ligand.

Gelinas, A.D.Davies, D.R.Edwards, T.E.Rohloff, J.C.Carter, J.D.Zhang, C.Gupta, S.Ishikawa, Y.Hirota, M.Nakaishi, Y.Jarvis, T.C.Janjic, N.

(2014) J.Biol.Chem. 289: 8720-8734

  • DOI: 10.1074/jbc.M113.532697
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • IL-6 is a secreted cytokine that functions through binding two cell surface receptors, IL-6Rα and gp130. Because of its involvement in the progression of several chronic inflammatory diseases, IL-6 is a target of pharmacologic interest. We have recen ...

    IL-6 is a secreted cytokine that functions through binding two cell surface receptors, IL-6Rα and gp130. Because of its involvement in the progression of several chronic inflammatory diseases, IL-6 is a target of pharmacologic interest. We have recently identified a novel class of ligands called SOMAmers (S low Off-rate Modified Aptamers) that bind IL-6 and inhibit its biologic activity. SOMAmers exploit the chemical diversity of protein-like side chains assembled on flexible nucleic acid scaffolds, resulting in an expanded repertoire of intra- and intermolecular interactions not achievable with conventional aptamers. Here, we report the co-crystal structure of a high affinity SOMAmer (Kd = 0.20 nm) modified at the 5-position of deoxyuridine in a complex with IL-6. The SOMAmer, comprised of a G-quartet domain and a stem-loop domain, engages IL-6 in a clamp-like manner over an extended surface exhibiting close shape complementarity with the protein. The interface is characterized by substantial hydrophobic interactions overlapping the binding surfaces of the IL-6Rα and gp130 receptors. The G-quartet domain retains considerable binding activity as a disconnected autonomous fragment (Kd = 270 nm). A single substitution from our diversely modified nucleotide library leads to a 37-fold enhancement in binding affinity of the G-quartet fragment (Kd = 7.4 nm). The ability to probe ligand surfaces in this manner is a powerful tool in the development of new therapeutic reagents with improved pharmacologic properties. The SOMAmer·IL-6 structure also expands our understanding of the diverse structural motifs achievable with modified nucleic acid libraries and elucidates the nature with which these unique ligands interact with their protein targets.


    Organizational Affiliation

    From the SomaLogic, Inc., Boulder, Colorado 80301.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Interleukin-6
A, C
186Homo sapiensMutation(s): 0 
Gene Names: IL6 (IFNB2)
Find proteins for P05231 (Homo sapiens)
Go to Gene View: IL6
Go to UniProtKB:  P05231
Entity ID: 1
MoleculeChainsLengthOrganism
SOMAmer SL1025B,D32N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
A2M
Query on A2M
B, D
RNA LINKINGC11 H16 N5 O7 PA
OMC
Query on OMC
B, D
RNA LINKINGC10 H16 N3 O8 PC
UPE
Query on UPE
B, D
DNA linkingC18 H22 N3 O9 PDU
2JU
Query on 2JU
B, D
DNA LINKINGC21 H22 N3 O9 P

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OMG
Query on OMG
B, D
RNA LINKINGC11 H16 N5 O8 PG
DUZ
Query on DUZ
B, D
DNA linkingC17 H20 N3 O9 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.186 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 69.020α = 90.00
b = 69.020β = 90.00
c = 108.470γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2014-02-12
    Type: Database references
  • Version 1.2: 2014-04-09
    Type: Database references
  • Version 1.3: 2016-06-01
    Type: Structure summary