8YDD

Crystal structure of Nanog(R100A) in complex with Wdr5

Summary for 8YDD

• Entry DOI: 10.2210/pdb8ydd/pdb
• Descriptor: WD repeat-containing protein 5, Homeobox protein NANOG (3 entities in total)
• Functional Keywords: transcription factor, protein-protein interaction, nuclear protein
• Biological source: Mus musculus (house mouse); More
• Total number of polymer chains: 5
• Total formula weight: 118060.50

Authors

Wang, D.,Shi, X.,Zhao, L.,Wu, B.,Chen, Y. (deposition date: 2024-02-20, release date: 2025-03-26, Last modification date: 2026-02-04)

Primary citation

Wang, D.,Shi, X.,Xie, J.,Zhao, L.,Wu, B.,Dong, Q.,Huang, Y.,Suo, J.,Wang, X.,He, B.,Yan, S.,Xue, H.,Shi, Y.,Liu, Y.,Wang, J.,Chen, Y.,Li, Y.
WDR5 remodels NANOG condensates to drive transcriptional programs and sustain stem cell identity.
Nat Commun, 2026

PubMed Abstract: Stem cell pluripotency relies on a finely tuned interplay between transcription factors and epigenetic regulators. Here, we identify a direct interaction between NANOG, a master pluripotency transcription factor, and WDR5, a core chromatin regulator essential for maintaining stem cell identity. Mechanistically, WDR5 remodels irregular NANOG aggregates into dynamic, liquid-liquid phase-separated condensates at pluripotency-associated promoters to activate target genes. Structural analyses show that the NANOG homeodomain engages WDR5 through an extended interface distinct from previously characterized short linear motifs. The NANOG R153A mutation disrupts this interaction, leading to impaired condensate formation, reduced chromatin co-occupancy, and diminished levels of active histone marks, ultimately compromising embryonic stem cell pluripotency. Pharmacological inhibition of the WDR5-NANOG interaction suppresses leukemia stem cell expansion in vivo, highlighting its therapeutic potential. Collectively, this study reveals that WDR5-dependent regulation of NANOG condensate dynamics links phase-separated assemblies to transcriptional control of stem cell identity in physiological and pathological contexts.

PubMed: 41565645
DOI: 10.1038/s41467-026-68623-w

Experimental method

X-RAY DIFFRACTION (2.5 Å)