9JQG | pdb_00009jqg

Crystal structure of rice DWARF14 in complex with Cyclo(L-Leu-L-Pro)

• PDB DOI: https://doi.org/10.2210/pdb9JQG/pdb

• Classification: HYDROLASE
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-27 Released: 2025-05-21 
• Deposition Author(s): Wang, Q.X., Wang, M.Y., Gao, S., Wang, B., Bai, Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.189 (Depositor) 
• R-Value Work: 
  0.169 (Depositor) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Root microbiota regulates tiller number in rice.

Zhang, J., Wang, B., Xu, H., Liu, W., Yu, J., Wang, Q., Yu, H., Wei, J.W., Dai, R., Zhou, J., He, Y., Zou, D., Yang, J., Ban, X., Hu, Q., Meng, X., Liu, Y.X., Wang, B., Hu, B., Wang, M., Xin, P., Chu, J., Li, C., Garrido-Oter, R., Yu, P., van Dijk, A.D.J., Dong, L., Bouwmeester, H., Gao, S., Huang, A., Chu, C., Li, J., Bai, Y.

(2025) Cell 188: 3152-3166.e16

• PubMed: 40267905 
• DOI: https://doi.org/10.1016/j.cell.2025.03.033
• Primary Citation of Related Structures:  
  9JQG


• PubMed Abstract: 
  

  Rice tillering is an important agronomic trait regulated by plant genetic and environmental factors. However, the role and mechanism of the root microbiota in modulating rice tillering have not been explored. Here, we examined the root microbiota composition and tiller numbers of 182 genome-sequenced rice varieties grown under field conditions and uncovered a significant correlation between root microbiota composition and rice tiller number. Using cultivated bacterial isolates, we demonstrated that various members of the root microbiota can regulate rice tillering in both laboratory and field conditions. Genetic, biochemical, and structural analyses revealed that cyclo(Leu-Pro), produced by the tiller-inhibiting bacterium Exiguobacterium R2567, activates the rice strigolactone (SL) signaling pathway by binding to the SL receptor OsD14, thus regulating tillering. The present work provides insight into how the root microbiota regulates key agronomic traits and offers a promising strategy for optimizing crop growth by harnessing the root microbiota in sustainable agriculture.

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Organizational Affiliation: 
• Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Gene Function and Modulation Research, Peking-Tsinghua-NIBS Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100101, China.
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Gene Function and Modulation Research, Peking-Tsinghua-NIBS Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100101, China.
Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Integrated Traditional Chinese and Western Medicine Research Center, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
Yazhouwan National Laboratory, Sanya 572024, China.
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, Yunnan University, Kunming 650504, China.
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100101, China.
Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Gene Function and Modulation Research, Peking-Tsinghua-NIBS Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China.
Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops and Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China.
State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, China.
Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany.
Plant Genetics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany.
Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, the Netherlands.
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Integrated Traditional Chinese and Western Medicine Research Center, Sun Yat-sen University Cancer Center, Guangzhou 510060, China. Electronic address: [e-mail].
Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China. Electronic address: [e-mail].
Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops and Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China. Electronic address: [e-mail].
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Yazhouwan National Laboratory, Sanya 572024, China. Electronic address: [e-mail].
Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Gene Function and Modulation Research, Peking-Tsinghua-NIBS Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.04 kDa 
• Atom Count: 4,883 
• Modeled Residue Count: 538 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Strigolactone esterase D14	A, B	269	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 EC: 3.1
UniProt
Find proteins for Q10QA5 (Oryza sativa subsp. japonica) Explore Q10QA5  Go to UniProtKB:  Q10QA5

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EBP (Subject of Investigation/LOI)	C [auth A]	(3~{S},8~{a}~{S})-3-(2-methylpropyl)-2,3,6,7,8,8~{a}-hexahydropyrrolo[1,2-a]pyrazine-1,4-dione C11 H18 N2 O2 SZJNCZMRZAUNQT-IUCAKERBSA-N
BEZ	G [auth A]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N
GOL	D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BU1	I [auth A]	1,4-BUTANEDIOL C4 H10 O2 WERYXYBDKMZEQL-UHFFFAOYSA-N
PGO	N [auth B]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N
PDO	H [auth A], M [auth B]	1,3-PROPANDIOL C3 H8 O2 YPFDHNVEDLHUCE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.189 (Depositor) 
• R-Value Work:  0.169 (Depositor) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.093	α = 90
b = 88.56	β = 90
c = 119.202	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Wang, Q.X., Wang, M.Y., Gao, S., Wang, B., Bai, Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2022YFF1001800
National Natural Science Foundation of China (NSFC)	China	32320103002 and 82173098 to S.G

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release
  
• Version 1.1: 2025-06-25
  Changes: Database references
• Version 1.2: 2025-08-27
  Changes: Structure summary