[English] 日本語
Yorodumi
- EMDB-34607: NARROW LEAF 1-close from Japonica -

+
Open data


ID or keywords:

Loading...

-
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-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_34607.png

Downloads & links

-
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 °

-
Supplemental data

-
Mask #1

Fileemd_34607_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
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)

-
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)

-
Sample components

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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.

-
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

+
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: 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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more