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- PDB-8hau: NARROW LEAF 1 from Indica -

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Basic information

Entry
Database: PDB / ID: 8hau
TitleNARROW LEAF 1 from Indica
ComponentsProtein NARROW LEAF 1
KeywordsSURFACTANT PROTEIN / Rice / panicle shape / photosynthetic efficiency / auxin transport
Function / homology
Function and homology information


stem vascular tissue pattern formation / internode patterning / regulation of leaf development / leaf vascular tissue pattern formation / nucleoplasm / cytoplasm
Similarity search - Function
NARROW LEAF 1 N-terminal domain / Nal1 C-terminal domain / Peptidase S1, PA clan
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Uncharacterized protein
Similarity search - Component
Biological speciesOryza sativa Indica Group (long-grained rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsZhang, S.J. / He, Y.J. / Wang, N. / Zhang, W.J. / Liu, C.M.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDA24020103-2 China
CitationJournal: To Be Published
Title: NARROW LEAF 1 from Indica
Authors: Zhang, S.J. / He, Y.J. / Wang, N. / Zhang, W.J. / Liu, C.M.
History
DepositionOct 26, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein NARROW LEAF 1
B: Protein NARROW LEAF 1
C: Protein NARROW LEAF 1
D: Protein NARROW LEAF 1
E: Protein NARROW LEAF 1
F: Protein NARROW LEAF 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,24612
Polymers237,2036
Non-polymers3,0436
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Protein NARROW LEAF 1


Mass: 39533.832 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Indica Group (long-grained rice)
Gene: OsI_17391 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2XXI5
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NARROW LEAF 1 from Indica / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 379.37 kDa/nm / Experimental value: YES
Source (natural)Organism: Oryza sativa Indica Group (long-grained rice)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: The grid was coated with gold prior to use / Grid material: NICKEL / Grid mesh size: 300 divisions/in. / Grid type: Homemade
VitrificationInstrument: 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
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: 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 recordingAverage 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
IDNameVersionCategoryDetails
1cryoSPARC4.0.2particle selectioncryoSPARC Blob picker was used to automatically select particle images.
4cryoSPARC4.0.2CTF correction
7cryoSPARC4.0.2model fitting
9cryoSPARC4.0.2model refinement
10cryoSPARC4.0.2initial Euler assignment
11cryoSPARC4.0.2final Euler assignment
12cryoSPARC4.0.2classification
13cryoSPARC4.0.23D reconstruction
CTF correctionDetails: CTF amplitude correction wae performed following 3D reconstruction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2347148
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 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 buildingB value: 192.4 / Protocol: AB INITIO MODEL / Space: REAL / Details: Initial local fitting was done using ChimeraX
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00516488
ELECTRON MICROSCOPYf_angle_d0.68422411
ELECTRON MICROSCOPYf_dihedral_angle_d4.4232243
ELECTRON MICROSCOPYf_chiral_restr0.0472543
ELECTRON MICROSCOPYf_plane_restr0.0042880

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