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- EMDB-23791: Subtomogram average of Photosystem II 2D semicrystalline array on... -

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Basic information

Entry
Database: EMDB / ID: EMD-23791
TitleSubtomogram average of Photosystem II 2D semicrystalline array on thylakoid membranes isolated from Phaeodactylum tricornutum
Map dataSubtomogram average of Photosystem II 2D semicrystalline array on thylakoid membranes isolated from Phaeodactylum tricornutum
Sample
  • Complex: Photosystem II 2D semicrystalline array
Biological speciesPhaeodactylum tricornutum CCAP 1055/1 (Diatom)
Methodsubtomogram averaging / cryo EM / Resolution: 37.0 Å
AuthorsJiang J / Cheong KY / Falkowski PG / Dai W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM116789-01A1 United States
CitationJournal: J Struct Biol / Year: 2021
Title: Integrating on-grid immunogold labeling and cryo-electron tomography to reveal photosystem II structure and spatial distribution in thylakoid membranes.
Authors: Jennifer Jiang / Kuan Yu Cheong / Paul G Falkowski / Wei Dai /
Abstract: A long-standing challenge in cell biology is elucidating the structure and spatial distribution of individual membrane-bound proteins, protein complexes and their interactions in their native ...A long-standing challenge in cell biology is elucidating the structure and spatial distribution of individual membrane-bound proteins, protein complexes and their interactions in their native environment. Here, we describe a workflow that combines on-grid immunogold labeling, followed by cryo-electron tomography (cryoET) imaging and structural analyses to identify and characterize the structure of photosystem II (PSII) complexes. Using an antibody specific to a core subunit of PSII, the D1 protein (uniquely found in the water splitting complex in all oxygenic photoautotrophs), we identified PSII complexes in biophysically active thylakoid membranes isolated from a model marine diatom Phaeodactylum tricornutum. Subsequent cryoET analyses of these protein complexes resolved two PSII structures: supercomplexes and dimeric cores. Our integrative approach establishes the structural signature of multimeric membrane protein complexes in their native environment and provides a pathway to elucidate their high-resolution structures.
History
DepositionApr 6, 2021-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateJul 7, 2021-
Current statusJul 7, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23791.png

Downloads & links

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Map

FileDownload / File: emd_23791.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of Photosystem II 2D semicrystalline array on thylakoid membranes isolated from Phaeodactylum tricornutum
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.45 Å/pix.
x 96 pix.
= 523.584 Å		5.45 Å/pix.
x 96 pix.
= 523.584 Å		5.45 Å/pix.
x 96 pix.
= 523.584 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.454 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.06625009 - 0.08565781
Average (Standard dev.)0.0016584306 (±0.010706886)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 523.58405 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.4545.4545.454
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z523.584523.584523.584
α/β/γ90.00090.00090.000
start NX/NY/NZ-210-210-210
NX/NY/NZ420420420
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
D min/max/mean-0.0660.0860.002

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Supplemental data

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Sample components

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Entire : Photosystem II 2D semicrystalline array

EntireName: Photosystem II 2D semicrystalline array
Components
  • Complex: Photosystem II 2D semicrystalline array

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Supramolecule #1: Photosystem II 2D semicrystalline array

SupramoleculeName: Photosystem II 2D semicrystalline array / type: complex / ID: 1 / Parent: 0
Details: On thylakoid membranes isolated from Phaeodactylum tricornutum
Source (natural)Organism: Phaeodactylum tricornutum CCAP 1055/1 (Diatom)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state2D array

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 49000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 37.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 263
ExtractionNumber tomograms: 1 / Number images used: 263
CTF correctionSoftware - Name: EMAN2
Final angle assignmentType: NOT APPLICABLE

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