Crystal structure of rice NAL1

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

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Serine protease NAL1 exerts pleiotropic functions through degradation of TOPLESS-related corepressor in rice.

Li, W.Yan, J.Zhang, Y.Zhang, F.Guan, Z.Yao, Y.Chang, Y.Tu, H.Li, X.Wang, H.Xiong, H.Lai, X.Yin, P.Xiong, L.

(2023) Nat Plants 9: 1130-1142

  • DOI: https://doi.org/10.1038/s41477-023-01449-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    NARROW LEAF 1 (NAL1) is a breeding-valuable pleiotropic gene that affects multiple agronomic traits in rice, although the molecular mechanism is largely unclear. Here, we report that NAL1 is a serine protease and displays a novel hexameric structure consisting of two ATP-mediated doughnut-shaped trimeric complexes. Moreover, we identified TOPLESS-related corepressor OsTPR2 involved in multiple growth and development processes as the substrate of NAL1. We found that NAL1 degraded OsTPR2, thus modulating the expression of downstream genes related to hormone signalling pathways, eventually achieving its pleiotropic physiological function. An elite allele, NAL1 A , which may have originated from wild rice, could increase grain yield. Furthermore, the NAL1 homologues in different crops have a similar pleiotropic function to NAL1. Our study uncovers a NAL1-OsTPR2 regulatory module and provides gene resources for the design of high-yield crops.

  • Organizational Affiliation

    National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
435Oryza sativaMutation(s): 6 
Gene Names: NAL1GFPLSCHL4SPIKEOs04g0615000LOC_Os04g52479OsJ_16147
Find proteins for B4XT64 (Oryza sativa subsp. japonica)
Explore B4XT64 
Go to UniProtKB:  B4XT64
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4XT64
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.413α = 90
b = 194.4β = 90
c = 173.374γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31700203

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-08-09
    Changes: Database references
  • Version 1.2: 2024-05-29
    Changes: Data collection