[English] 日本語
Yorodumi
- EMDB-2939: Electron tomogram of Pseudomonas moraviensis stanleyae containing... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2939
TitleElectron tomogram of Pseudomonas moraviensis stanleyae containing selenium nanoparticles
Map dataReconstruction of Pseudomonas moraviensis stanleyae containing selenium nanoparticles
Sample
  • Sample: Selenium Nanoparticles contained within cells of Pseudomonas moraviensis stanleyae
  • Em label: Pseudomonas moraviensis stanleyae
KeywordsPseudomonas moraviensis stanleyae / selenium nanoparticle / electron tomography
Methodelectron tomography
AuthorsNi TW / Staicu L / Nemeth RS / Schwartz C / Crawford D / Seligman JD / Hunter WJ / Pilon-Smits E / Ackerson CJ
CitationJournal: Nanoscale / Year: 2015
Title: Progress toward clonable inorganic nanoparticles.
Authors: Thomas W Ni / Lucian C Staicu / Richard S Nemeth / Cindi L Schwartz / David Crawford / Jeffrey D Seligman / William J Hunter / Elizabeth A H Pilon-Smits / Christopher J Ackerson /
Abstract: Pseudomonas moraviensis stanleyae was recently isolated from the roots of the selenium (Se) hyperaccumulator plant Stanleya pinnata. This bacterium tolerates normally lethal concentrations of SeO3(2-) ...Pseudomonas moraviensis stanleyae was recently isolated from the roots of the selenium (Se) hyperaccumulator plant Stanleya pinnata. This bacterium tolerates normally lethal concentrations of SeO3(2-) in liquid culture, where it also produces Se nanoparticles. Structure and cellular ultrastructure of the Se nanoparticles as determined by cellular electron tomography shows the nanoparticles as intracellular, of narrow dispersity, symmetrically irregular and without any observable membrane or structured protein shell. Protein mass spectrometry of a fractionated soluble cytosolic material with selenite reducing capability identified nitrite reductase and glutathione reductase homologues as NADPH dependent candidate enzymes for the reduction of selenite to zerovalent Se nanoparticles. In vitro experiments with commercially sourced glutathione reductase revealed that the enzyme can reduce SeO3(2-) (selenite) to Se nanoparticles in an NADPH-dependent process. The disappearance of the enzyme as determined by protein assay during nanoparticle formation suggests that glutathione reductase is associated with or possibly entombed in the nanoparticles whose formation it catalyzes. Chemically dissolving the nanoparticles releases the enzyme. The size of the nanoparticles varies with SeO3(2-) concentration, varying in size form 5 nm diameter when formed at 1.0 μM [SeO3(2-)] to 50 nm maximum diameter when formed at 100 μM [SeO3(2-)]. In aggregate, we suggest that glutathione reductase possesses the key attributes of a clonable nanoparticle system: ion reduction, nanoparticle retention and size control of the nanoparticle at the enzyme site.
History
DepositionMar 17, 2015-
Header (metadata) releaseApr 1, 2015-
Map releaseSep 23, 2015-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_2939.map.gz / Format: CCP4 / Size: 270.4 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationReconstruction of Pseudomonas moraviensis stanleyae containing selenium nanoparticles
Voxel sizeX=Y=Z: 91 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)9.528561590000001 (±31.384305950000002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-44-2114
Dimensions12001228197
Spacing12001228197
CellA: 111748.0 Å / B: 109200.0 Å / C: 17927.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z919191
M x/y/z12281200197
origin x/y/z0.0000.0000.000
length x/y/z111748.000109200.00017927.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-21-4414
NC/NR/NS12281200197
D min/max/mean-128.000127.0009.529

-
Supplemental data

-
Sample components

-
Entire : Selenium Nanoparticles contained within cells of Pseudomonas mora...

EntireName: Selenium Nanoparticles contained within cells of Pseudomonas moraviensis stanleyae
Components
  • Sample: Selenium Nanoparticles contained within cells of Pseudomonas moraviensis stanleyae
  • Em label: Pseudomonas moraviensis stanleyae

-
Supramolecule #1000: Selenium Nanoparticles contained within cells of Pseudomonas mora...

SupramoleculeName: Selenium Nanoparticles contained within cells of Pseudomonas moraviensis stanleyae
type: sample / ID: 1000
Details: Cells were grown in 10 mM HNaSeO3/LB for 36 hours. Medium was replaced every 8 hours.
Number unique components: 1

-
Macromolecule #1: Pseudomonas moraviensis stanleyae

MacromoleculeName: Pseudomonas moraviensis stanleyae / type: em_label / ID: 1
Details: ~80 nm selenium nanoparticles were made inside of Pseudomonas moraviensis stanleyae cells. Showing a potential clonable tag capable of making inorganic nanoparticles.

-
Experimental details

-
Structure determination

Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.4 / Details: 20 mM Tris, 2% glutaraldehyde, 2.5% formaldehyde
GridDetails: Formvar coated copper slot grid
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° / Tilt series - Axis1 - Angle increment: 1 °
DateApr 12, 2014
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 120
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

Final reconstructionSoftware - Name: Etomo / Number images used: 120

+
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