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Open data
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Basic information
Entry | Database: PDB / ID: 8hau | ||||||
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Title | NARROW LEAF 1 from Indica | ||||||
![]() | Protein NARROW LEAF 1 | ||||||
![]() | 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 / ADENOSINE-5'-TRIPHOSPHATE / Uncharacterized protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å | ||||||
![]() | Zhang, S.J. / He, Y.J. / Wang, N. / Zhang, W.J. / Liu, C.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: NARROW LEAF 1 from Indica 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 400.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 71.4 KB | Display | |
Data in CIF | ![]() | 101.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 34609MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 39533.832 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: OsI_17391 / Production host: ![]() ![]() #2: Chemical | ChemComp-ATP / Has ligand of interest | Y | |
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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 |
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Sample preparation
Component | Name: NARROW LEAF 1 from Indica / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 379.37 kDa/nm / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
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: NICKEL / Grid mesh size: 300 divisions/in. / Grid type: Homemade |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: Vitrification carried out in Ethane |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 57000 X / Calibrated magnification: 57000 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 |
Image recording | Average exposure time: 1.68 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 3179 |
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Processing
EM software |
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CTF correction | Details: CTF amplitude correction wae performed following 3D reconstruction Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2347148 | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D3 (2x3 fold dihedral) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1273195 / 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: 192.4 / Protocol: AB INITIO MODEL / Space: REAL / Details: Initial local fitting was done using ChimeraX | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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