[English] 日本語
Yorodumi
- EMDB-0616: Cryo-electron tomography of marine bacterium Candidatus Thioglobu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0616
TitleCryo-electron tomography of marine bacterium Candidatus Thioglobus singularis strain PS1
Map datamarine bacterium Candidatus Thioglobus singularis strain PS1
Sample
  • Cell: Marine bacteria Candidatus Thioglobus singularis strain PS1
    • Complex: PilQ
Biological speciesCandidatus Thioglobus singularis PS1 (bacteria)
Methodelectron tomography / cryo EM
AuthorsNicastro D / Zhao X
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)OCE-1232840 United States
CitationJournal: Environ Microbiol / Year: 2019
Title: Heterotrophic carbon metabolism and energy acquisition in Candidatus Thioglobus singularis strain PS1, a member of the SUP05 clade of marine Gammaproteobacteria.
Authors: Rachel L Spietz / Rachel A Lundeen / Xiaowei Zhao / Daniela Nicastro / Anitra E Ingalls / Robert M Morris /
Abstract: A hallmark of the SUP05 clade of marine Gammaproteobacteria is the ability to use energy obtained from reduced inorganic sulfur to fuel autotrophic fixation of carbon using RuBisCo. However, some ...A hallmark of the SUP05 clade of marine Gammaproteobacteria is the ability to use energy obtained from reduced inorganic sulfur to fuel autotrophic fixation of carbon using RuBisCo. However, some SUP05 also have the genetic potential for heterotrophic growth, raising questions about the roles of SUP05 in the marine carbon cycle. We used genomic reconstructions, physiological growth experiments and proteomics to characterize central carbon and energy metabolism in Candidatus Thioglobus singularis strain PS1, a representative from the SUP05 clade that has the genetic potential for autotrophy and heterotrophy. Here, we show that the addition of individual organic compounds and 0.2 μm filtered diatom lysate significantly enhanced the growth of this bacterium. This positive growth response to organic substrates, combined with expression of a complete TCA cycle, heterotrophic pathways for carbon assimilation, and methylotrophic pathways for energy conversion demonstrate strain PS1's capacity for heterotrophic growth. Further, our inability to verify the expression of RuBisCO suggests that carbon fixation was not critical for growth. These results highlight the metabolic diversity of the SUP05 clade that harbours both primary producers and consumers of organic carbon in the oceans and expand our understanding of specific pathways of organic matter oxidation by the heterotrophic SUP05.
History
Header (metadata) releaseFeb 20, 2019-
DepositionFeb 24, 2019-
Map releaseApr 17, 2019-
UpdateAug 12, 2020-
Current statusAug 12, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_0616.map.gz / Format: CCP4 / Size: 2 GB / Type: IMAGE STORED AS SIGNED BYTE
Annotationmarine bacterium Candidatus Thioglobus singularis strain PS1
Voxel sizeX=Y=Z: 5.5 Å
Density
Minimum - Maximum-128 - 127
Average (Standard dev.)33.395523 (±58.3291)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-666-467172
Dimensions27012101381
Spacing21012701381
CellA: 11555.5 Å / B: 14855.5 Å / C: 2095.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z5.55.55.5
M x/y/z21012701381
origin x/y/z0.0000.0000.000
length x/y/z11555.50014855.5002095.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-467-666172
NC/NR/NS21012701381
D min/max/mean-128.000127.00033.396

-
Supplemental data

-
Sample components

-
Entire : Marine bacteria Candidatus Thioglobus singularis strain PS1

EntireName: Marine bacteria Candidatus Thioglobus singularis strain PS1
Components
  • Cell: Marine bacteria Candidatus Thioglobus singularis strain PS1
    • Complex: PilQ

-
Supramolecule #1: Marine bacteria Candidatus Thioglobus singularis strain PS1

SupramoleculeName: Marine bacteria Candidatus Thioglobus singularis strain PS1
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Candidatus Thioglobus singularis PS1 (bacteria) / Strain: PS1

-
Supramolecule #2: PilQ

SupramoleculeName: PilQ / type: complex / ID: 2 / Parent: 1 / Details: outer membrane pore complex
Source (natural)Organism: Candidatus Thioglobus singularis PS1 (bacteria) / Strain: PS1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7 / Details: artificial sea water
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 5.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
Details: The grid was washed with ethyl acetate prior to glow discharge.
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Instrument: GATAN CRYOPLUNGE 3
DetailsCells were harvested by centrifugation at 39,000xg at 4 degrees Celsius for 1 hour.
Cryo protectantNo
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aldrich / Diameter: 10 nm

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Detector mode: COUNTING / Average exposure time: 5.6 sec. / Average electron dose: 1.52 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 0.5 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 26000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 61

+
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://pdbjlvh1.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