Summary information

PDB id
4ni9
Class
cytokine-DNA
Method
X-ray (2.55 Å)
Summary
Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (somamer sl1025), form 2
Reference
Gelinas AD, Davies DR, Edwards TE, Rohloff JC, Carter JD, Zhang C, Gupta S, Ishikawa Y, Hirota M, Nakaishi Y, Jarvis TC, Janjic N (2014): "Crystal structure of interleukin-6 in complex with a modified nucleic Acid ligand." J.Biol.Chem., 289, 8720-8734. doi: 10.1074/jbc.M113.532697.
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 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.
G4 notes
4 G-tetrads, 2 G4 helices, 2 G4 stems, 2(+Ln+Lw+Ln), chair(2+2), UDUD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.693 type=other  nts=4 GGGg B.DG1,B.DG32,B.DG10,B.OMG6
 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.718 type=bowl   nts=4 GGGG B.DG2,B.DG31,B.DG11,B.DG5
 3 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.672 type=other  nts=4 GGGg D.DG1,D.DG32,D.DG10,D.OMG6
 4 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.625 type=bowl-2 nts=4 GGGG D.DG2,D.DG31,D.DG11,D.DG5

List of 2 G4-helices

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGg B.DG1,B.DG32,B.DG10,B.OMG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG B.DG2,B.DG31,B.DG11,B.DG5
  step#1  mm(<>,outward)  area=16.12 rise=3.54 twist=14.6
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG B.DG1,B.DG2
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG B.DG32,B.DG31
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG B.DG10,B.DG11
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 gG B.OMG6,B.DG5

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGg B.DG1,B.DG32,B.DG10,B.OMG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG B.DG2,B.DG31,B.DG11,B.DG5
  step#1  mm(<>,outward)  area=16.12 rise=3.54 twist=14.6

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Helix#2, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGg D.DG1,D.DG32,D.DG10,D.OMG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG D.DG2,D.DG31,D.DG11,D.DG5
  step#1  mm(<>,outward)  area=17.40 rise=3.70 twist=13.5
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG D.DG1,D.DG2
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG D.DG32,D.DG31
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG D.DG10,D.DG11
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 gG D.OMG6,D.DG5

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGg D.DG1,D.DG32,D.DG10,D.OMG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG D.DG2,D.DG31,D.DG11,D.DG5
  step#1  mm(<>,outward)  area=17.40 rise=3.70 twist=13.5

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List of 2 G4-stems

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGg B.DG1,B.DG32,B.DG10,B.OMG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG B.DG2,B.DG31,B.DG11,B.DG5
  step#1  mm(<>,outward)  area=16.12 rise=3.54 twist=14.6
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG B.DG1,B.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG B.DG32,B.DG31
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG B.DG10,B.DG11
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 gG B.OMG6,B.DG5
  loop#1 type=lateral   strands=[#1,#4] nts=2 cA B.OMC3,B.DA4
  loop#2 type=lateral   strands=[#4,#3] nts=3 ttt B.DUZ7,B.DUZ8,B.UPE9
  loop#3 type=lateral   strands=[#3,#2] nts=19 tAttaACacGttAAGtcGt B.2JU12,B.DA13,B.DUZ14,B.DUZ15,B.A2M16,B.DA17,B.DC18,B.A2M19,B.OMC20,B.DG21,B.DUZ22,B.DUZ23,B.DA24,B.DA25,B.DG26,B.DUZ27,B.OMC28,B.DG29,B.DUZ30

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Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGg D.DG1,D.DG32,D.DG10,D.OMG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG D.DG2,D.DG31,D.DG11,D.DG5
  step#1  mm(<>,outward)  area=17.40 rise=3.70 twist=13.5
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG D.DG1,D.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG D.DG32,D.DG31
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG D.DG10,D.DG11
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 gG D.OMG6,D.DG5
  loop#1 type=lateral   strands=[#1,#4] nts=2 cA D.OMC3,D.DA4
  loop#2 type=lateral   strands=[#4,#3] nts=3 ttt D.DUZ7,D.DUZ8,D.UPE9
  loop#3 type=lateral   strands=[#3,#2] nts=19 tAttaACacGttAAGtcGt D.2JU12,D.DA13,D.DUZ14,D.DUZ15,D.A2M16,D.DA17,D.DC18,D.A2M19,D.OMC20,D.DG21,D.DUZ22,D.DUZ23,D.DA24,D.DA25,D.DG26,D.DUZ27,D.OMC28,D.DG29,D.DUZ30

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