8PN2

CryoEM structure of Nal1 protein, allele IR64, from Oryza sativa indica cultivar

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


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 

  • 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.

    • 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.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein NARROW LEAF 1
A, B, C, D, E
A, B, C, D, E, F
586Oryza sativa Indica GroupMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4XT64
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP
Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
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)
Query on MG
Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
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: 2.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_4903
RECONSTRUCTIONRELION4.0

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China32071291, 32201042, 32071225, 31870788
Centre National de la Recherche Scientifique (CNRS)FranceIRP "Helicase-mediated Gquadruplex DNA unwinding and genome stability"

Revision History  (Full details and data files)

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