8PMI

Structure of Nal1 indica cultivar IR64, construct 36-458 in presence of peptide from FZP protein

PDB DOI: https://doi.org/10.2210/pdb8PMI/pdb

Classification: PLANT PROTEIN
Organism(s): Oryza sativa Indica Group
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2023-06-28 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.83 Å
R-Value Free: 0.268
R-Value Work: 0.206
R-Value Observed: 0.209

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

PubMed: 38600265 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 281.67 kDa
Atom Count: 19,159
Modelled Residue Count: 2,449
Deposited Residue Count: 2,538
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein NARROW LEAF 1	A, B, C, D, E A, B, C, D, E, F	423	Oryza sativa Indica Group	Mutation(s): 1 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4XT64
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain Z [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth E]	CA [auth F] G [auth A] K [auth B] R [auth C] V [auth D] CA [auth F], G [auth A], K [auth B], R [auth C], V [auth D], Z [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain CA [auth F] Focus chain G [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain G [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D]	EA [auth F] FA [auth F] I [auth A] J [auth A] N [auth B] EA [auth F], FA [auth F], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], T [auth C], U [auth C], X [auth D], Y [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth F] Focus chain FA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain EA [auth F] Focus chain FA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain DA [auth F] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D]	AA [auth E] DA [auth F] H [auth A] L [auth B] M [auth B] AA [auth E], DA [auth F], H [auth A], L [auth B], M [auth B], S [auth C], W [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain W [auth D]
NH4 Query on NH4 Download Ideal Coordinates CCD File SDF format, chain BA [auth E] MOL2 format, chain BA [auth E]	BA [auth E]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain BA [auth E] Interactions & Density Focus chain BA [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.83 Å
R-Value Free: 0.268
R-Value Work: 0.206
R-Value Observed: 0.209
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.276	α = 90
b = 189.186	β = 90
c = 89.922	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

Huang, L.Y.

Rety, S.

Xi, X.G.

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 (Full details and data files)

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

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Help and Resources

8PMI

Structure of Nal1 indica cultivar IR64, construct 36-458 in presence of peptide from FZP protein

The catalytic triad of rice NARROW LEAF1 involves H234.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)