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- EMDB-34607: NARROW LEAF 1-close from Japonica -

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Basic information

Entry
Database: EMDB / ID: EMD-34607
TitleNARROW LEAF 1-close from Japonica
Map dataElectron Microscopy Volume Map of Protein NARROW LEAF 1.
Sample
  • Complex: NARROW LEAF 1-close from Japonica
    • Protein or peptide: Protein NARROW LEAF 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 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-close from Japonica
Authors: Zhang SJ / He YJ / Wang N / Zhang WJ / Liu CM
History
DepositionOct 26, 2022-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34607.png

Downloads & links

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Map

FileDownload / File: emd_34607.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationElectron Microscopy Volume Map of Protein NARROW LEAF 1.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 214.76 Å		1.07 Å/pix.
x 200 pix.
= 214.76 Å		1.07 Å/pix.
x 200 pix.
= 214.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0738 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-2.2660682 - 2.6409729
Average (Standard dev.)0.0012466637 (±0.107208274)
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_34607_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Electron Microscopy Half Map A of Protein NARROW LEAF 1.

Fileemd_34607_half_map_1.map
AnnotationElectron Microscopy Half Map A of Protein NARROW LEAF 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Electron Microscopy Half Map B of Protein NARROW LEAF 1.

Fileemd_34607_half_map_2.map
AnnotationElectron Microscopy Half Map B of Protein NARROW LEAF 1.
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-close from Japonica

EntireName: NARROW LEAF 1-close from Japonica
Components
  • Complex: NARROW LEAF 1-close from Japonica
    • Protein or peptide: Protein NARROW LEAF 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: NARROW LEAF 1-close from Japonica

SupramoleculeName: NARROW LEAF 1-close from Japonica / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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 Japonica Group (Japanese rice)
Molecular weightTheoretical: 63.317902 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKPSDDKAQL SGLAQSEESS LDVDHQSFPC SPSIQPVASG CTHTENSAAY FLWPTSNLQH CAAEGRANYF GNLQKGLLPR HPGRLPKGQ QANSLLDLMT IRAFHSKILR RFSLGTAVGF RIRKGDLTDI PAILVFVARK VHKKWLNPAQ CLPAILEGPG G VWCDVDVV ...String:
MKPSDDKAQL SGLAQSEESS LDVDHQSFPC SPSIQPVASG CTHTENSAAY FLWPTSNLQH CAAEGRANYF GNLQKGLLPR HPGRLPKGQ QANSLLDLMT IRAFHSKILR RFSLGTAVGF RIRKGDLTDI PAILVFVARK VHKKWLNPAQ CLPAILEGPG G VWCDVDVV EFSYYGAPAQ TPKEQMFSEL VDKLCGSDEC IGSGSQVASH ETFGTLGAIV KRRTGNKQVG FLTNHHVAVD LD YPNQKMF HPLPPNLGPG VYLGAVERAT SFITDDVWYG IYAGTNPETF VRADGAFIPF ADDFDISTVT TVVRGVGDIG DVK VIDLQC PLNSLIGRQV CKVGRSSGHT TGTVMAYALE YNDEKGICFF TDILVVGENR QTFDLEGDSG SLIILTSQDG EKPR PIGII WGGTANRGRL KLTSDHGPEN WTSGVDLGRL LDRLELDIII TNESLQDAVQ QQRFALVAAV TSAVGESSGV PVAIP EEKI EEIFEPLGIQ IQQLPRHDVA ASGTEGEEAS NTVVNVEEHQ FISNFVGMSP VRDDQDAPRS ITNLNNPSEE ELAMSL HLG DREPKRLRSD SGSSLDLEK

UniProtKB: Protein NARROW LEAF 1

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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
CTF correctionSoftware - Name: cryoSPARC (ver. 4.0.2)
Details: CTF amplitude correction was performed following 3D reconstruction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.89 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: 670053
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: 153.3
Output model

PDB-8has:
NARROW LEAF 1-close from Japonica

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