[English] 日本語
Yorodumi
- EMDB-34609: NARROW LEAF 1 from Indica -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34609
TitleNARROW LEAF 1 from Indica
Map dataProtein NARROW LEAF 1 from Indica Density Map by cryo-EM.
Sample
  • Complex: NARROW LEAF 1 from Indica
    • Protein or peptide: Protein NARROW LEAF 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsRice / panicle shape / photosynthetic efficiency / auxin transport / SURFACTANT PROTEIN
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
Uncharacterized protein
Similarity search - Component
Biological speciesOryza sativa Indica Group (long-grained rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 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 from Indica
Authors: Zhang SJ / He YJ / Wang N / Zhang WJ / Liu CM
History
DepositionOct 26, 2022-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_34609.png

Downloads & links

-
Map

FileDownload / File: emd_34609.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationProtein NARROW LEAF 1 from Indica Density Map by cryo-EM.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 150 pix.
= 213. Å		1.42 Å/pix.
x 150 pix.
= 213. Å		1.42 Å/pix.
x 150 pix.
= 213. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65
Minimum - Maximum-5.2315836 - 5.9686174
Average (Standard dev.)-0.0012152658 (±0.22224902)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 213.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_34609_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Protein NARROW LEAF 1 from Indica Volume Mask B by cryo-EM.

Fileemd_34609_half_map_1.map
AnnotationProtein NARROW LEAF 1 from Indica Volume Mask B by cryo-EM.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Protein NARROW LEAF 1 from Indica Volume Mask A by cryo-EM.

Fileemd_34609_half_map_2.map
AnnotationProtein NARROW LEAF 1 from Indica Volume Mask A by cryo-EM.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : NARROW LEAF 1 from Indica

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

-
Supramolecule #1: NARROW LEAF 1 from Indica

SupramoleculeName: NARROW LEAF 1 from Indica / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oryza sativa Indica Group (long-grained rice)
Molecular weightTheoretical: 379.37 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 Indica Group (long-grained rice)
Molecular weightTheoretical: 39.533832 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: QQANSLLDLM TIRAFHSKIL RRFSLGTAVG FRIRKGDLTD IPAILVFVAR KVHKKWLNPA QCLPAILEGP GGVWCDVDVV EFSYYGAPA QTPKEQMFSE LVDKLCGSDE CIGSGSQVAS HETFGTLGAI VKRRTGNKQV GFLTNRHVAV DLDYPNQKMF H PLPPNLGP ...String:
QQANSLLDLM TIRAFHSKIL RRFSLGTAVG FRIRKGDLTD IPAILVFVAR KVHKKWLNPA QCLPAILEGP GGVWCDVDVV EFSYYGAPA QTPKEQMFSE LVDKLCGSDE CIGSGSQVAS HETFGTLGAI VKRRTGNKQV GFLTNRHVAV DLDYPNQKMF H PLPPNLGP GVYLGAVERA TSFITDDVWY GIYAGTNPET FVRADGAFIP FADDFDISTV TTVVRGVGDI GDVKVIDLQC PL NSLIGRQ VCKVGRSSGH TTGTVMAYAL EYNDEKGICF FTDILVVGEN RQTFDLEGDS GSLIILTSQD GEKPRPIGII WGG TANRGR LKLTSDHGPE NWTSGVDLGR LLDRLELDII ITNESL

UniProtKB: Uncharacterized protein

-
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: Homemade / Material: NICKEL / Mesh: 300 / Support film - Material: GOLD / 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 TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 3179 / Average exposure time: 1.68 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 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: 57000 / 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: 57000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2347148
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.02 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: 1273195
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: 192.4
Output model

PDB-8hau:
NARROW LEAF 1 from Indica

+
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