+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34608 | |||||||||
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Title | NARROW LEAF 1-open from Japonica | |||||||||
Map data | Protein NARROW LEAF 1-Open from Japonica Density Map by cryo-EM. | |||||||||
Sample |
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Keywords | 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 / Protein NARROW LEAF 1 Function and homology information | |||||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) / Oryza sativa subsp. japonica (Japanese rice) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.03 Å | |||||||||
Authors | Zhang SJ / He YJ / Wang N / Zhang WJ / Liu CM | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: NARROW LEAF 1-open from Japonica 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 | emd_34608.map.gz | 28.8 MB | EMDB map data format | |
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Header (meta data) | emd-34608-v30.xml emd-34608.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
Images | emd_34608.png | 37.7 KB | ||
Masks | emd_34608_msk_1.map | 30.5 MB | Mask map | |
Filedesc metadata | emd-34608.cif.gz | 6.1 KB | ||
Others | emd_34608_half_map_1.map.gz emd_34608_half_map_2.map.gz | 28.3 MB 28.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34608 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34608 | HTTPS FTP |
-Validation report
Summary document | emd_34608_validation.pdf.gz | 905.7 KB | Display | EMDB validaton report |
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Full document | emd_34608_full_validation.pdf.gz | 905.2 KB | Display | |
Data in XML | emd_34608_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_34608_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34608 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34608 | HTTPS FTP |
-Related structure data
Related structure data | 8hatMC 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_34608.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Protein NARROW LEAF 1-Open from Japonica Density Map by cryo-EM. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0738 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34608_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Protein NARROW LEAF 1-Open from Japonica Half Map B by cryo-EM.
File | emd_34608_half_map_1.map | ||||||||||||
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Annotation | Protein NARROW LEAF 1-Open from Japonica Half Map B by cryo-EM. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Protein NARROW LEAF 1-Open from Japonica Half Map A by cryo-EM.
File | emd_34608_half_map_2.map | ||||||||||||
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Annotation | Protein NARROW LEAF 1-Open from Japonica Half Map A by cryo-EM. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NARROW LEAF 1-open from Japonica
Entire | Name: NARROW LEAF 1-open from Japonica |
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Components |
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-Supramolecule #1: NARROW LEAF 1-open from Japonica
Supramolecule | Name: NARROW LEAF 1-open from Japonica / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Oryza sativa Japonica Group (Japanese rice) |
Molecular weight | Theoretical: 379.51 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: Oryza sativa subsp. japonica (Japanese rice) |
Molecular weight | Theoretical: 44.683582 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: SAAYFLWPTS NLQHCAAEGR ANYFGNLQKG LLPRHPGRLP KGQQANSLLD LMTIRAFHSK ILRRFSLGTA VGFRIRKGDL TDIPAILVF VARKVHKKWL NPAQCLPAIL EGPGGVWCDV DVVEFSYYGA PAQTPKEQMF SELVDKLCGS DECIGSGSQV A SHETFGTL ...String: SAAYFLWPTS NLQHCAAEGR ANYFGNLQKG LLPRHPGRLP KGQQANSLLD LMTIRAFHSK ILRRFSLGTA VGFRIRKGDL TDIPAILVF VARKVHKKWL NPAQCLPAIL EGPGGVWCDV DVVEFSYYGA PAQTPKEQMF SELVDKLCGS DECIGSGSQV A SHETFGTL GAIVKRRTGN KQVGFLTNHH VAVDLDYPNQ KMFHPLPPNL GPGVYLGAVE RATSFITDDV WYGIYAGTNP ET FVRADGA FIPFADDFDI STVTTVVRGV GDIGDVKVID LQCPLNSLIG RQVCKVGRSS GHTTGTVMAY ALEYNDEKGI CFF TDILVV GENRQTFDLE GDSGSLIILT SQDGEKPRPI GIIWGGTANR GRLKLTSDHG PENWTSGVDL GRLLDRLELD IIIT NESLQ DAVQ UniProtKB: Protein NARROW LEAF 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.0 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / 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. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 3770 / Average exposure time: 0.972 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 22500 / 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: 22500 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+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: 130.8 |
Output model | PDB-8hat: |