+Open data
-Basic information
Entry | Database: PDB / ID: 8hat | ||||||
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Title | NARROW LEAF 1-open from Japonica | ||||||
Components | Protein NARROW LEAF 1 | ||||||
Keywords | SURFACTANT PROTEIN / Rice / panicle shape / photosynthetic efficiency / auxin transport | ||||||
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 subsp. japonica (Japanese rice) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å | ||||||
Authors | Zhang, S.J. / He, Y.J. / Wang, N. / Zhang, W.J. / Liu, C.M. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: NARROW LEAF 1-open from Japonica Authors: Zhang, S.J. / He, Y.J. / Wang, N. / Zhang, W.J. / Liu, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hat.cif.gz | 420.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hat.ent.gz | 342.6 KB | Display | PDB format |
PDBx/mmJSON format | 8hat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hat_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8hat_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8hat_validation.xml.gz | 83 KB | Display | |
Data in CIF | 8hat_validation.cif.gz | 118.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/8hat ftp://data.pdbj.org/pub/pdb/validation_reports/ha/8hat | HTTPS FTP |
-Related structure data
Related structure data | 34608MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 44683.582 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: NAL1, GFP, LSCHL4, SPIKE, Os04g0615000, LOC_Os04g52479, OsJ_16147 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4XT64 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: NARROW LEAF 1-open from Japonica / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 379.51 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Oryza sativa Japonica Group (Japanese rice) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 8 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: The grid was coated with gold prior to use / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: Vitrification carried out in Ethane |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Calibrated magnification: 22500 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 0.972 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 3770 |
-Processing
EM software |
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Image processing | Details: The selected images were high-pass filtered and normalized | ||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: CTF amplitude correction was performed following 3D reconstruction Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4503713 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 330894 / Algorithm: FOURIER SPACE Details: The version 4.0.2 of the cryoSPARC program was used for the reconstruction Num. of class averages: 3 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 130.8 / Protocol: AB INITIO MODEL / Space: REAL / Details: Initial local fitting was done using ChimeraX | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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