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- EMDB-0513: Subtomogram average of S_layer structure on the outer membrane su... -

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Basic information

Entry
Database: EMDB / ID: EMD-0513
TitleSubtomogram average of S_layer structure on the outer membrane surface of Thioglobus autotrophicus EF1 cell
Map dataS_layer structure on the outer membrane surface of Thioglobus autotrophicus EF1 cell
Sample
  • Complex: S_layer structure on the outer membrane surface of Thioglobus autotrophicus EF1 cell
    • Complex: hypothetical protein
Biological speciesCandidatus Thioglobus autotrophicus (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 35.0 Å
AuthorsNicastro D / Zhao XW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)OCE-1232840 United States
CitationJournal: mBio / Year: 2019
Title: Morphological Plasticity in a Sulfur-Oxidizing Marine Bacterium from the SUP05 Clade Enhances Dark Carbon Fixation.
Authors: Vega Shah / Xiaowei Zhao / Rachel A Lundeen / Anitra E Ingalls / Daniela Nicastro / Robert M Morris /
Abstract: Sulfur-oxidizing bacteria from the SUP05 clade are abundant in anoxic and oxygenated marine waters that appear to lack reduced sources of sulfur for cell growth. This raises questions about how these ...Sulfur-oxidizing bacteria from the SUP05 clade are abundant in anoxic and oxygenated marine waters that appear to lack reduced sources of sulfur for cell growth. This raises questions about how these chemosynthetic bacteria survive across oxygen and sulfur gradients and how their mode of survival impacts the environment. Here, we use growth experiments, proteomics, and cryo-electron tomography to show that a SUP05 isolate, " Thioglobus autotrophicus," is amorphous in shape and several times larger and stores considerably more intracellular sulfur when it respires oxygen. We also show that these cells can use diverse sources of reduced organic and inorganic sulfur at submicromolar concentrations. Enhanced cell size, carbon content, and metabolic activity of the aerobic phenotype are likely facilitated by a stabilizing surface-layer (S-layer) and an uncharacterized form of FtsZ-less cell division that supports morphological plasticity. The additional sulfur storage provides an energy source that allows cells to continue metabolic activity when exogenous sulfur sources are not available. This metabolic flexibility leads to the production of more organic carbon in the ocean than is estimated based solely on their anaerobic phenotype. Identifying shifts in microbial metabolism across redox gradients will improve efforts to model marine oxygen minimum zone (OMZ) ecosystems. Here, we show that aerobic morphology and metabolism increase cell size, sulfur storage capacity, and carbon fixation rates in " Thioglobus autotrophicus," a chemosynthetic bacterium from the SUP05 clade that crosses oxic-anoxic boundaries.
History
DepositionJan 30, 2019-
Header (metadata) releaseFeb 20, 2019-
Map releaseDec 18, 2019-
UpdateAug 12, 2020-
Current statusAug 12, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 155
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 155
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0513.png

Downloads & links

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Map

FileDownload / File: emd_0513.map.gz / Format: CCP4 / Size: 766.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationS_layer structure on the outer membrane surface of Thioglobus autotrophicus EF1 cell
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.5 Å/pix.
x 40 pix.
= 220. Å		5.5 Å/pix.
x 70 pix.
= 385. Å		5.5 Å/pix.
x 70 pix.
= 385. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 5.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 155 / Movie #1: 155
Minimum - Maximum151.28079 - 159.33499
Average (Standard dev.)154.22632 (±0.69535565)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions707040
Spacing707040
CellA: 385.0 Å / B: 385.0 Å / C: 220.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.55.55.5
M x/y/z707040
origin x/y/z0.0000.0000.000
length x/y/z385.000385.000220.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS707040
D min/max/mean151.281159.335154.226

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Supplemental data

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Sample components

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Entire : S_layer structure on the outer membrane surface of Thioglobus aut...

EntireName: S_layer structure on the outer membrane surface of Thioglobus autotrophicus EF1 cell
Components
  • Complex: S_layer structure on the outer membrane surface of Thioglobus autotrophicus EF1 cell
    • Complex: hypothetical protein

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Supramolecule #1: S_layer structure on the outer membrane surface of Thioglobus aut...

SupramoleculeName: S_layer structure on the outer membrane surface of Thioglobus autotrophicus EF1 cell
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Candidatus Thioglobus autotrophicus (bacteria) / Strain: EF1

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Supramolecule #2: hypothetical protein

SupramoleculeName: hypothetical protein / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Candidatus Thioglobus autotrophicus (bacteria) / Strain: EF1

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Instrument: GATAN CRYOPLUNGE 3
DetailsT. autotrophicus strain EF1 cells were harvested by centrifuging at 39,000 x g, at 4 degree for 1 hour.

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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

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD / Number subtomograms used: 1840
ExtractionNumber tomograms: 6 / Number images used: 1840
Final angle assignmentType: OTHER

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