9IIB | pdb_00009iib

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

PDB DOI: https://doi.org/10.2210/pdb9IIB/pdb

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

Deposited: 2024-06-19 Released: 2025-12-24
Deposition Author(s): Ruan, Y., Dong, S., Zhang, Y., Jeremy, M.
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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.252 (Depositor), 0.251 (DCC)
R-Value Work:
0.221 (Depositor), 0.222 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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 Search on PubMed
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.

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.

Macromolecule Content

Total Structure Weight: 101.32 kDa
Atom Count: 6,571
Modeled Residue Count: 816
Deposited Residue Count: 864
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LysR family transcriptional regulator	A, B, C, D	216	Rhizobium leguminosarum	Mutation(s): 0 Gene Names: GUK36_35585
UniProt
Find proteins for A0A6P0BW74 (Rhizobium leguminosarum) Explore A0A6P0BW74 Go to UniProtKB: A0A6P0BW74
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6P0BW74
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6JP (Subject of Investigation/LOI) Query on 6JP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth D] SDF format, chain L [auth D] SDF format, chain J [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C]	F [auth A] H [auth B] I [auth B] J [auth C] K [auth D] F [auth A], H [auth B], I [auth B], J [auth C], K [auth D], L [auth D]	(2S)-5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)-2,3-dihydro-4H-1-benzopyran-4-one C₁₆ H₁₄ O₆ AIONOLUJZLIMTK-AWEZNQCLSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.252 (Depositor), 0.251 (DCC)
R-Value Work: 0.221 (Depositor), 0.222 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.42	α = 90
b = 197.708	β = 90
c = 50.468	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

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