5UC6

Structural insights into IL-1 alpha recognition by a naphthyl-modified aptamer that mimics IL-1RI Domain III


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 3.0 of the entry. See complete history

Literature

Structural basis for IL-1 alpha recognition by a modified DNA aptamer that specifically inhibits IL-1 alpha signaling.

Ren, X.Gelinas, A.D.von Carlowitz, I.Janjic, N.Pyle, A.M.

(2017) Nat Commun 8: 810-810

  • DOI: 10.1038/s41467-017-00864-2

  • PubMed Abstract: 
  • IL-1α is an essential cytokine that contributes to inflammatory responses and is implicated in various forms of pathogenesis and cancer. Here we report a naphthyl modified DNA aptamer that specifically binds IL-1α and inhibits its signaling pathway. ...

    IL-1α is an essential cytokine that contributes to inflammatory responses and is implicated in various forms of pathogenesis and cancer. Here we report a naphthyl modified DNA aptamer that specifically binds IL-1α and inhibits its signaling pathway. By solving the crystal structure of the IL-1α/aptamer, we provide a high-resolution structure of this critical cytokine and we reveal its functional interaction interface with high-affinity ligands. The non-helical aptamer, which represents a highly compact nucleic acid structure, contains a wealth of new conformational features, including an unknown form of G-quadruplex. The IL-1α/aptamer interface is composed of unusual polar and hydrophobic elements, along with an elaborate hydrogen bonding network that is mediated by sodium ion. IL-1α uses the same interface to interact with both the aptamer and its cognate receptor IL-1RI, thereby suggesting a novel route to immunomodulatory therapeutics.The cytokine interleukin 1α (IL-1α) plays an important role in inflammatory processes. Here the authors use SELEX to generate a modified DNA aptamer which specifically binds IL-1α, present the structure of the IL-1α/aptamer complex and show that this aptamer inhibits the IL-1α signaling pathway.


    Organizational Affiliation

    Department of Chemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT, 06511, USA. anna.pyle@yale.edu.,Department of Chemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT, 06511, USA.,SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO, 80301, USA.,Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA.,Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA. anna.pyle@yale.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interleukin-1 alpha
A
159Homo sapiensMutation(s): 0 
Gene Names: IL1A (IL1F1)
Find proteins for P01583 (Homo sapiens)
Go to Gene View: IL1A
Go to UniProtKB:  P01583
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*G)-R(P*(85Y))-D(P*GP*AP*G)-R(P*(85Y)P*(85Y))-D(P*A)-R(P*(85Y))-D(P*GP*GP*G)-R(P*(85Y)P*(85Y))-D(P*AP*GP*AP*G)-R(P*(85Y))-D(P*CP*GP*(ATD))-3')B23synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ATD
Query on ATD
B
DNA LINKINGC10 H15 N2 O8 PDT
85Y
Query on 85Y
B
RNA linkingC21 H22 N3 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.178 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.790α = 90.00
b = 74.790β = 90.00
c = 86.360γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-12-21 
  • Released Date: 2017-10-11 
  • Deposition Author(s): Ren, X., Pyle, A.

Funding OrganizationLocationGrant Number
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Database references
  • Version 2.0: 2017-11-15
    Type: Atomic model, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2018-08-22
    Type: Atomic model, Data collection, Derived calculations