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Open data
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Basic information
Entry | Database: PDB / ID: 8has | ||||||
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Title | NARROW LEAF 1-close from Japonica | ||||||
![]() | Protein NARROW LEAF 1 | ||||||
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Function / homology | stem vascular tissue pattern formation / internode patterning / regulation of leaf development / leaf vascular tissue pattern formation / Peptidase S1, PA clan / ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, S.J. / He, Y.J. / Wang, N. / Zhang, W.J. / Liu, C.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: NARROW LEAF 1-close 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 427.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 34607MC 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: 63317.902 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: NAL1, GFP, LSCHL4, SPIKE, Os04g0615000, LOC_Os04g52479, OsJ_16147 Production host: ![]() ![]() ![]() #2: Chemical | ChemComp-ATP / ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: NARROW LEAF 1-close from Japonica / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 379.51 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![]() ![]() |
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 |
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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![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
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 |
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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![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 670053 / Algorithm: FOURIER SPACE Details: The version 4.0.2 of the cryoSPARC program was used for the reconstruction Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 153.3 / Protocol: AB INITIO MODEL / Space: REAL / Details: Initial local fitting was done using ChimeraX | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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