9X6W | pdb_00009x6w

Crystal structure of NodD-EBD (Effector Binding Domain) from Rhizobium leguminosarum bv. vicae 3841

• PDB DOI: https://doi.org/10.2210/pdb9X6W/pdb

• Classification: TRANSCRIPTION
• Organism(s): Rhizobium leguminosarum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-10-16 Released: 2025-12-24 
• Deposition Author(s): Ruan, Y., Dong, S., Zhang, Y., Murray, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), The Ministry of Science and Technology, Shanghai Science and Technology Commission, Basic Research Zone Program of Shanghai, CAS Project for Young Scientists in Basic Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.253 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: in silico

Literature

The molecular basis of the binding and specific activation of rhizobial NodD by flavonoids.

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.

(2026) Science 391: 184-189

• PubMed: 41505558 
• DOI: https://doi.org/10.1126/science.aec3061
• Primary Citation of Related Structures:  
  9IIB, 9X6W


• 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 Pisum sativum (pea) symbiont Rhizobium leguminosarum NodD revealed two pockets that are essential for its activation by flavonoids. Comparative studies with NodD1 of Sinorhizobium medicae , the symbiont of Medicago truncatula , 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 S. medicae NodD1 in the R. leguminosarum NodD backbone was sufficient to complement nitrogen fixation in M. truncatula by an S. medicae nodD1 mutant, confirming the critical role of flavonoid recognition in host range.

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Organizational Affiliation: 
• CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai, China.
University of Chinese Academy of Sciences, Beijing, China.
The State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; Shanghai Academy of Natural Sciences (SANS), Shanghai, China.
Department of Plant Sciences, University of Oxford, Oxford, UK.
College of Life Sciences, Shanghai Normal University, Shanghai, China.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 201.67 kDa 
• Atom Count: 12,943 
• Modeled Residue Count: 1,694 
• Deposited Residue Count: 1,760 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LysR family transcriptional regulator	A, B, C, D, E, F, G, H	220	Rhizobium leguminosarum	Mutation(s): 0  Gene Names: GUK36_35585
UniProt
Find proteins for A0A6P0BW74 (Rhizobium leguminosarum) Explore A0A6P0BW74  Go to UniProtKB:  A0A6P0BW74

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.253 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 192.774	α = 90
b = 192.774	β = 90
c = 153.297	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPX	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Ruan, Y., Dong, S., Zhang, Y., Murray, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32150710527
The Ministry of Science and Technology	China	2024YFA0918203
Shanghai Science and Technology Commission	China	22JC1410800
Basic Research Zone Program of Shanghai	China	JCYJ-SHFY-2022-012
CAS Project for Young Scientists in Basic Research	China	YSBR-011

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release
  
• Version 1.1: 2026-01-21
  Changes: Database references