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- EMDB-17768: CryoEM structure of Nal1 protein, allele IR64, from Oryza sativa ... -

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Basic information

Entry
Database: EMDB / ID: EMD-17768
TitleCryoEM structure of Nal1 protein, allele IR64, from Oryza sativa indica cultivar
Map data
Sample
  • Complex: Nal1
    • Protein or peptide: Protein NARROW LEAF 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsSerine protease / PLANT PROTEIN
Function / homologystem vascular tissue pattern formation / internode patterning / regulation of leaf development / leaf vascular tissue pattern formation / Peptidase S1, PA clan / nucleoplasm / cytoplasm / Protein NARROW LEAF 1
Function and homology information
Biological speciesOryza sativa Japonica Group (Japanese rice) / Oryza sativa Indica Group (long-grained rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsHuang LY / Rety S / Xi XG
Funding support China, France, 2 items
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, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17768.png

Downloads & links

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Map

FileDownload / File: emd_17768.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.171
Minimum - Maximum-1.818517 - 3.3567443
Average (Standard dev.)0.0011039417 (±0.07396374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_17768_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17768_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Nal1

EntireName: Nal1
Components
  • Complex: Nal1
    • Protein or peptide: Protein NARROW LEAF 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Nal1

SupramoleculeName: Nal1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)

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Macromolecule #1: Protein NARROW LEAF 1

MacromoleculeName: Protein NARROW LEAF 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Indica Group (long-grained rice)
Molecular weightTheoretical: 63.822469 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: FHMKPSDDKA QLSGLAQSEE SSLDVDHQSF PCSPSIQPVA SGCTHTENSA AYFLWPTSNL QHCAAEGRAN YFGNLQKGLL PRHPGRLPK GQQANSLLDL MTIRAFHSKI LRRFSLGTAV GFRIRKGDLT DIPAILVFVA RKVHKKWLNP AQCLPAILEG P GGVWCDVD ...String:
FHMKPSDDKA QLSGLAQSEE SSLDVDHQSF PCSPSIQPVA SGCTHTENSA AYFLWPTSNL QHCAAEGRAN YFGNLQKGLL PRHPGRLPK GQQANSLLDL MTIRAFHSKI LRRFSLGTAV GFRIRKGDLT DIPAILVFVA RKVHKKWLNP AQCLPAILEG P GGVWCDVD VVEFSYYGAP AQTPKEQMFS ELVDKLCGSD ECIGSGSQVA SHETFGTLGA IVKRRTGNKQ VGFLTNRHVA VD LDYPNQK MFHPLPPNLG PGVYLGAVER ATSFITDDVW YGIYAGTNPE TFVRADGAFI PFADDFDIST VTTVVRGVGD IGD VKVIDL QCPLNSLIGR QVCKVGRSSG HTTGTVMAYA LEYNDEKGIC FFTDILVVGE NRQTFDLEGD SGSLIILTSQ DGEK PRPIG IIWGGTANRG RLKLTSDHGP ENWTSGVDLG RLLDRLELDI IITNESLQDA VQQQRFALVA AVTSAVGESS GAPVA IPEE KVEEIFEPLG IQIQQLPRHD VAASGTEGEE ASNTVVNVEE HQFISNFVGM SPVRDDQDAP RSITNLNNPS EEELAM SLH LGDREPKRLR SDSGSSLDLE KLE

UniProtKB: Protein NARROW LEAF 1

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5 / Details: 20mM Tris-HCl 100mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 282 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
SoftwareName: SerialEM (ver. 3.8.4)
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 700 / Average electron dose: 49.02 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 50.0 µm / Nominal defocus min: 5.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 216590
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8pme

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 203380
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8pme


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: PHENIX (ver. 1.21rc1_4903)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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