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Yorodumi- EMDB-17768: CryoEM structure of Nal1 protein, allele IR64, from Oryza sativa ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17768 | |||||||||
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Title | CryoEM structure of Nal1 protein, allele IR64, from Oryza sativa indica cultivar | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Serine protease / PLANT PROTEIN | |||||||||
Function / homology | stem 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 species | Oryza sativa Japonica Group (Japanese rice) / Oryza sativa Indica Group (long-grained rice) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.63 Å | |||||||||
Authors | Huang LY / Rety S / Xi XG | |||||||||
Funding support | China, France, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17768.map.gz | 203.8 MB | EMDB map data format | |
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Header (meta data) | emd-17768-v30.xml emd-17768.xml | 17 KB 17 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17768_fsc.xml | 12.6 KB | Display | FSC data file |
Images | emd_17768.png | 134.1 KB | ||
Filedesc metadata | emd-17768.cif.gz | 6.5 KB | ||
Others | emd_17768_half_map_1.map.gz emd_17768_half_map_2.map.gz | 200.2 MB 200.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17768 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17768 | HTTPS FTP |
-Related structure data
Related structure data | 8pn2MC 8pmeC 8pmgC 8pmiC 8pmlC 8pmmC 8pn1C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17768.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_17768_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17768_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Nal1
Entire | Name: Nal1 |
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Components |
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-Supramolecule #1: Nal1
Supramolecule | Name: Nal1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Oryza sativa Japonica Group (Japanese rice) |
-Macromolecule #1: Protein NARROW LEAF 1
Macromolecule | Name: Protein NARROW LEAF 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryza sativa Indica Group (long-grained rice) |
Molecular weight | Theoretical: 63.822469 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: 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 |
-Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 / Details: 20mM Tris-HCl 100mM NaCl |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 282 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 50.0 µm / Nominal defocus min: 5.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Software | Name: SerialEM (ver. 3.8.4) |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 700 / Average electron dose: 49.02 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |