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- PDB-8pn2: CryoEM structure of Nal1 protein, allele IR64, from Oryza sativa ... -

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Basic information

Entry
Database: PDB / ID: 8pn2
TitleCryoEM structure of Nal1 protein, allele IR64, from Oryza sativa indica cultivar
ComponentsProtein NARROW LEAF 1
KeywordsPLANT PROTEIN / Serine protease
Function / homologystem vascular tissue pattern formation / internode patterning / regulation of leaf development / leaf vascular tissue pattern formation / Peptidase S1, PA clan / nucleoplasm / cytoplasm / ADENOSINE-5'-TRIPHOSPHATE / Protein NARROW LEAF 1
Function and homology information
Biological speciesOryza sativa Indica Group (long-grained rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsHuang, L.Y. / Rety, S. / Xi, X.G.
Funding support China, France, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32071291, 32201042, 32071225, 31870788 China
Centre National de la Recherche Scientifique (CNRS)IRP "Helicase-mediated Gquadruplex DNA unwinding and genome stability" France
CitationJournal: Nat Plants / Year: 2024
Title: The catalytic triad of rice NARROW LEAF1 involves H234.
Authors: Ling-Yun Huang / Na-Nv Liu / Wei-Fei Chen / Xia Ai / Hai-Hong Li / Ze-Lin Zhang / Xi-Miao Hou / Philippe Fossé / Olivier Mauffret / Dong-Sheng Lei / Stephane Rety / Xu-Guang Xi /
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 ...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.
History
DepositionJun 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein NARROW LEAF 1
B: Protein NARROW LEAF 1
C: Protein NARROW LEAF 1
D: Protein NARROW LEAF 1
E: Protein NARROW LEAF 1
F: Protein NARROW LEAF 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)386,12418
Polymers382,9356
Non-polymers3,18912
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25350 Å2
ΔGint-149 kcal/mol
Surface area87420 Å2

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Components

#1: Protein
Protein NARROW LEAF 1 / Protein GREEN FOR PHOTOSYNTHESIS / Protein QUANTITATIVE TRAIT LOCUS FOR FLAG LEAF WIDTH 4 / qFLW4 / ...Protein GREEN FOR PHOTOSYNTHESIS / Protein QUANTITATIVE TRAIT LOCUS FOR FLAG LEAF WIDTH 4 / qFLW4 / Protein SPIKELET NUMBER


Mass: 63822.469 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Indica Group (long-grained rice)
Gene: NAL1, GFP, LSCHL4, SPIKE, Os04g0615000, LOC_Os04g52479, OsJ_16147
Plasmid: pET15b-sumo / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: B4XT64
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Nal1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 20mM Tris-HCl 100mM NaCl
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 282 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 50000 nm / Nominal defocus min: 5000 nm / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 49.02 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 700
Image scansMovie frames/image: 32

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2SerialEM3.8.4image acquisition
4RELION4CTF correction
7PHENIX1.21rc1_4903model fitting
9PHENIX1.21rc1_4903model refinement
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 216590
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 203380 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 8PME

8pme


Accession code: 8PME / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 39.58 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00218894
ELECTRON MICROSCOPYf_angle_d0.50125674
ELECTRON MICROSCOPYf_dihedral_angle_d5.4162562
ELECTRON MICROSCOPYf_chiral_restr0.0432856
ELECTRON MICROSCOPYf_plane_restr0.0033318

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