8PML

Structure of Nal1 protein , SPIKE allele from japonica rice, construct 46-458

• PDB DOI: https://doi.org/10.2210/pdb8PML/pdb

• Classification: PLANT PROTEIN
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2023-06-29 Released: 2024-04-17 
• Deposition Author(s): Huang, L.Y., Rety, S., Xi, X.G.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.252 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Starting Model: experimental

Literature

The catalytic triad of rice NARROW LEAF1 involves H234.

Huang, L.Y., Liu, N.N., Chen, W.F., Ai, X., Li, H.H., Zhang, Z.L., Hou, X.M., Fosse, P., Mauffret, O., Lei, D.S., Rety, S., Xi, X.G.

(2024) Nat Plants 10: 743-748

• PubMed: 38600265 
• DOI: https://doi.org/10.1038/s41477-024-01668-1
• Primary Citation of Related Structures:  
  8PME, 8PMG, 8PMI, 8PML, 8PMM, 8PN1, 8PN2


• PubMed Abstract: 
  

  NARROW LEAF1 (NAL1) exerts a multifaceted influence on leaf morphology and crop yield. Recent crystal study proposed that histidine 233 (H233) is part of the catalytic triad. Here we report that unlike suggested previously, H234 instead of H233 is a component of the catalytic triad alongside residues D291 and S385 in NAL1. Remarkably, residue 233 unexpectedly plays a pivotal role in regulating NAL1's proteolytic activity. These findings establish a strong foundation for utilizing NAL1 in breeding programs aimed at improving crop yield.

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Organizational Affiliation: 

College of Life Sciences, State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 274.46 kDa 
• Atom Count: 18,777 
• Modelled Residue Count: 2,411 
• Deposited Residue Count: 2,478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein NARROW LEAF 1	A, B, C, D, E, F	413	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: NAL1, GFP, LSCHL4, SPIKE, Os04g0615000, LOC_Os04g52479, OsJ_16147
UniProt
Find proteins for B4XT64 (Oryza sativa subsp. japonica) Explore B4XT64  Go to UniProtKB:  B4XT64

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.252 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.428	α = 90
b = 193.36	β = 90
c = 84.037	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Huang, L.Y., Rety, S., Xi, X.G.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32071291
National Natural Science Foundation of China (NSFC)	China	32201042
National Natural Science Foundation of China (NSFC)	China	32071225
National Natural Science Foundation of China (NSFC)	China	31870788

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release
  
• Version 1.1: 2024-04-24
  Changes: Database references
• Version 1.2: 2024-06-05
  Changes: Database references