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- EMDB-34608: NARROW LEAF 1-open from Japonica -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-34608
TitleNARROW LEAF 1-open from Japonica
Map dataProtein NARROW LEAF 1-Open from Japonica Density Map by cryo-EM.
Sample
  • Complex: NARROW LEAF 1-open from Japonica
    • Protein or peptide: Protein NARROW LEAF 1
KeywordsRice / panicle shape / photosynthetic efficiency / auxin transport / SURFACTANT PROTEIN
Function / homologystem 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 speciesOryza sativa Japonica Group (Japanese rice) / Oryza sativa subsp. japonica (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsZhang SJ / He YJ / Wang N / Zhang WJ / Liu CM
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDA24020103-2 China
CitationJournal: To Be Published
Title: NARROW LEAF 1-open from Japonica
Authors: Zhang SJ / He YJ / Wang N / Zhang WJ / Liu CM
History
DepositionOct 26, 2022-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34608.png

Downloads & links

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Map

FileDownload / File: emd_34608.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationProtein NARROW LEAF 1-Open from Japonica Density Map by cryo-EM.
Voxel sizeX=Y=Z: 1.0738 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.6765412 - 2.4141607
Average (Standard dev.)-0.00025767635 (±0.0660015)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 214.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34608_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Protein NARROW LEAF 1-Open from Japonica Half Map B by cryo-EM.

Fileemd_34608_half_map_1.map
AnnotationProtein NARROW LEAF 1-Open from Japonica Half Map B by cryo-EM.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Protein NARROW LEAF 1-Open from Japonica Half Map A by cryo-EM.

Fileemd_34608_half_map_2.map
AnnotationProtein NARROW LEAF 1-Open from Japonica Half Map A by cryo-EM.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NARROW LEAF 1-open from Japonica

EntireName: NARROW LEAF 1-open from Japonica
Components
  • Complex: NARROW LEAF 1-open from Japonica
    • Protein or peptide: Protein NARROW LEAF 1

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Supramolecule #1: NARROW LEAF 1-open from Japonica

SupramoleculeName: NARROW LEAF 1-open from Japonica / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 379.51 kDa/nm

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Macromolecule #1: Protein NARROW LEAF 1

MacromoleculeName: Protein NARROW LEAF 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)
Molecular weightTheoretical: 44.683582 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.0 mg/mL
BufferpH: 8
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Vitrification carried out in Ethane.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe selected images were high-pass filtered and normalized
Particle selectionNumber selected: 4503713
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.2)
Details: The version 4.0.2 of the cryoSPARC program was used for the reconstruction
Number images used: 330894
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.0.2)
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.0.2)
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC (ver. 4.0.2)

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Atomic model buiding 1

DetailsInitial local fitting was done using ChimeraX
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 130.8
Output model

PDB-8hat:
NARROW LEAF 1-open from Japonica

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