9IIB
Crystal structure of NodD-EBD (Effector Binding Domain) in complex with hesperetin from Rhizobium leguminosarum bv. vicae 3841
This is a non-PDB format compatible entry.
Summary for 9IIB
| Entry DOI | 10.2210/pdb9iib/pdb |
| Descriptor | LysR family transcriptional regulator, GLYCEROL, (2S)-5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)-2,3-dihydro-4H-1-benzopyran-4-one, ... (4 entities in total) |
| Functional Keywords | nodd, lysr transcription factors, flavonoids, rhizobia, transcription |
| Biological source | Rhizobium leguminosarum |
| Total number of polymer chains | 4 |
| Total formula weight | 101317.91 |
| Authors | Ruan, Y.,Dong, S.,Zhang, Y.,Jeremy, M. (deposition date: 2024-06-19, release date: 2025-12-24, Last modification date: 2026-01-21) |
| Primary citation | Ruan, Y.,Dong, S.,Jiang, S.,Wang, Y.,Wu, X.,Zhuang, Y.,Wu, W.,East, A.K.,Xu, P.,Poole, P.S.,Zhang, Y.,Murray, J.D. The molecular basis of the binding and specific activation of rhizobial NodD by flavonoids. Science, 391:184-189, 2026 Cited by PubMed Abstract: The specific partnership between legumes and rhizobia relies on a chemical dialogue. Plant flavonoids activate the bacterial transcription factor NodD, which triggers production of Nod factors that are recognized by the plant. Structural studies of the (pea) symbiont NodD revealed two pockets that are essential for its activation by flavonoids. Comparative studies with NodD1 of , the symbiont of , revealed that this specificity is determined by the shape of the pocket and by specific amino acids. A chimeric NodD containing the flavonoid recognition residues from NodD1 in the NodD backbone was sufficient to complement nitrogen fixation in by an mutant, confirming the critical role of flavonoid recognition in host range. PubMed: 41505558DOI: 10.1126/science.aec3061 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.75 Å) |
Structure validation
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