Related Experiment Video
Updated: Aug 2, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
Published on: September 17, 2017
Structural anomalies in a published NMR-derived structure of IRAK-M
Hessel Poelman1, Hans Ippel2, Berke Gürkan3
1Amsterdam UMC, University of Amsterdam, Medical Biochemistry, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands; Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands.
The Toll-Like Receptor and Interleukin-1 Receptor (IL1-R) pathway relies on MyD88 and IL-1R Associated Kinases (IRAKs). A new study identified structural anomalies in the IRAK-M death domain NMR structure (5UKE), proposing a refined model for better accuracy.
Area of Science:
- Molecular Biology
- Structural Biology
- Immunology
Background:
- Toll-Like Receptor (TLR) and Interleukin-1 Receptor (IL1-R) signaling pathways are crucial for innate immunity.
- These pathways involve MyD88 adaptor protein and IL-1R Associated Kinases (IRAKs), forming the Myddosome complex.
- Understanding the structure of IRAK-M death domain is vital for elucidating Myddosome assembly and signaling specificity.
Purpose of the Study:
- To analyze the structural integrity of the IRAK-M death domain monomer structure (PDBid: 5UKE) determined by NMR.
- To investigate potential structural anomalies in 5UKE that could impact downstream modeling and analysis.
- To develop an improved homology model of the IRAK-M death domain based on high-resolution X-ray structures.
Main Methods:
- Analysis of the IRAK-M death domain NMR structure (5UKE) using structure validation tools.
- Comparison of 5UKE with homologous high-resolution X-ray crystal structures.
- Homology modeling using Yasara, based on two high-resolution crystal structures of death domains.
Main Results:
- Identification of significant structural anomalies in the 5UKE NMR structure, including packing issues, frayed helices, and improbable side chain conformations.
- Demonstration that homology models based on 5UKE exhibit structural problems like disallowed torsion angles.
- Development of an alternative homology model for the IRAK-M death domain that better aligns with known structural data and deposited chemical shift data.
Conclusions:
- The IRAK-M death domain NMR structure (5UKE) contains notable structural inaccuracies.
- A refined homology model provides a more reliable structural representation of the IRAK-M death domain.
- This improved model is essential for accurate docking studies and understanding IRAK-M's role in Myddosome assembly and signaling selectivity.
Related Concept Videos
¹H NMR: Complex Splitting
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied first.
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution
IR Spectrum Peak Splitting: Symmetric vs Asymmetric Vibrations
IR Frequency Region: X–H Stretching
IR Frequency Region: Alkyne and Nitrile Stretching
Comparing the stretching vibrational frequency of C≡C triple bonds with that of double and single bonds, it is evident that C≡C triple bonds exhibit a higher stretching frequency than C=C double and C–C single bonds. Similarly, the C≡N triple bond exhibits higher stretching absorption than the C=N...
IR Frequency Region: Fingerprint Region
The...

