9JQG | pdb_00009jqg

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.189 (Depositor), 0.187 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • 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.


  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Strigolactone esterase D14
A, B
269Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: D14D88HTD2Os03g0203200LOC_Os03g10620
EC: 3.1
UniProt
Find proteins for Q10QA5 (Oryza sativa subsp. japonica)
Explore Q10QA5 
Go to UniProtKB:  Q10QA5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ10QA5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EBP (Subject of Investigation/LOI)
Query on A1EBP

Download Ideal Coordinates CCD File 
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
Query on BEZ

Download Ideal Coordinates CCD File 
G [auth A]BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
J [auth B]
K [auth B]
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
Query on BU1

Download Ideal Coordinates CCD File 
I [auth A]1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
PGO
Query on PGO

Download Ideal Coordinates CCD File 
N [auth B]S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
PDO
Query on PDO

Download Ideal Coordinates CCD File 
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), 0.187 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.093α = 90
b = 88.56β = 90
c = 119.202γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2022YFF1001800
National Natural Science Foundation of China (NSFC)China32320103002 and 82173098 to S.G

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Database references