8PN1

CryoEM structure of Nal1 protein, allele SPIKE, from Oryza sativa japonica group

• PDB DOI: https://doi.org/10.2210/pdb8PN1/pdb
• EM Map EMD-17766: EMDB EMDataResource

• 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 Science Foundation (NSF, China), Centre National de la Recherche Scientifique (CNRS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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 (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 286.81 kDa 
• Atom Count: 18,852 
• Modelled Residue Count: 2,418 
• Deposited Residue Count: 2,598 
• 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	433	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: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0
MODEL REFINEMENT	PHENIX	1.21rc1_4903

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 Science Foundation (NSF, China)	China	32071291, 32201042, 32071225, 31870788
Centre National de la Recherche Scientifique (CNRS)	France	IRP "Helicase-mediated Gquadruplex DNA unwinding and genome stability"

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