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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | NARROW LEAF 1 from Indica | |||||||||
![]() | Protein NARROW LEAF 1 from Indica Density Map by cryo-EM. | |||||||||
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![]() | Rice / panicle shape / photosynthetic efficiency / auxin transport / SURFACTANT 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 / Uncharacterized protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.02 Å | |||||||||
![]() | Zhang SJ / He YJ / Wang N / Zhang WJ / Liu CM | |||||||||
Funding support | ![]()
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![]() | ![]() Title: NARROW LEAF 1 from Indica Authors: Zhang SJ / He YJ / Wang N / Zhang WJ / Liu CM | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 12.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.3 KB 17.3 KB | Display Display | ![]() |
Images | ![]() | 550.6 KB | ||
Masks | ![]() | 12.9 MB | ![]() | |
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 11.9 MB 11.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 807.1 KB | Display | ![]() |
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Full document | ![]() | 806.6 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 10.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hauMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Protein NARROW LEAF 1 from Indica Density Map by cryo-EM. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.42 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Protein NARROW LEAF 1 from Indica Volume Mask B by cryo-EM.
File | emd_34609_half_map_1.map | ||||||||||||
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Annotation | Protein NARROW LEAF 1 from Indica Volume Mask B by cryo-EM. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Protein NARROW LEAF 1 from Indica Volume Mask A by cryo-EM.
File | emd_34609_half_map_2.map | ||||||||||||
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Annotation | Protein NARROW LEAF 1 from Indica Volume Mask A by cryo-EM. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : NARROW LEAF 1 from Indica
Entire | Name: NARROW LEAF 1 from Indica |
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Components |
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-Supramolecule #1: NARROW LEAF 1 from Indica
Supramolecule | Name: NARROW LEAF 1 from Indica / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 379.37 kDa/nm |
-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: ![]() ![]() |
Molecular weight | Theoretical: 39.533832 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QQANSLLDLM TIRAFHSKIL RRFSLGTAVG FRIRKGDLTD IPAILVFVAR KVHKKWLNPA QCLPAILEGP GGVWCDVDVV EFSYYGAPA QTPKEQMFSE LVDKLCGSDE CIGSGSQVAS HETFGTLGAI VKRRTGNKQV GFLTNRHVAV DLDYPNQKMF H PLPPNLGP ...String: QQANSLLDLM TIRAFHSKIL RRFSLGTAVG FRIRKGDLTD IPAILVFVAR KVHKKWLNPA QCLPAILEGP GGVWCDVDVV EFSYYGAPA QTPKEQMFSE LVDKLCGSDE CIGSGSQVAS HETFGTLGAI VKRRTGNKQV GFLTNRHVAV DLDYPNQKMF H PLPPNLGP GVYLGAVERA TSFITDDVWY GIYAGTNPET FVRADGAFIP FADDFDISTV TTVVRGVGDI GDVKVIDLQC PL NSLIGRQ VCKVGRSSGH TTGTVMAYAL EYNDEKGICF FTDILVVGEN RQTFDLEGDS GSLIILTSQD GEKPRPIGII WGG TANRGR LKLTSDHGPE NWTSGVDLGR LLDRLELDII ITNESL UniProtKB: Uncharacterized protein |
-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: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.0 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Homemade / Material: NICKEL / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: The grid was coated with gold prior to use |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Vitrification carried out in Ethane. |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 3179 / Average exposure time: 1.68 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 57000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 57000 |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Details | Initial local fitting was done using ChimeraX |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 192.4 |
Output model | ![]() PDB-8hau: |