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- EMDB-0539: Averaged structure of Photosystem II holocomplex on thylakoid mem... -

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Basic information

Entry
Database: EMDB / ID: EMD-0539
TitleAveraged structure of Photosystem II holocomplex on thylakoid membrane from diatom
Map dataAveraged structure of photosystem II holocomplex on thylakoid membrane from diatom
Sample
  • Organelle or cellular component: Thylakoid membrane purified from diatom
Biological speciesPhaeodactylum tricornutum (Diatom)
Methodsubtomogram averaging / cryo EM / Resolution: 26.0 Å
AuthorsChen M / Kuang X / Levitan O / Falkowski P / Dai W
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM08139 United States
National Institute of Health Midwest Consortium for High Resolution Cryo-electron MicroscopyU24 GM116789-01A1 United States
National Science Foundation (NSF, United States)Eager 1558128 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Structural and functional analyses of photosystem II in the marine diatom .
Authors: Orly Levitan / Muyuan Chen / Xuyuan Kuang / Kuan Yu Cheong / Jennifer Jiang / Melissa Banal / Nikhita Nambiar / Maxim Y Gorbunov / Steven J Ludtke / Paul G Falkowski / Wei Dai /
Abstract: A descendant of the red algal lineage, diatoms are unicellular eukaryotic algae characterized by thylakoid membranes that lack the spatial differentiation of stroma and grana stacks found in green ...A descendant of the red algal lineage, diatoms are unicellular eukaryotic algae characterized by thylakoid membranes that lack the spatial differentiation of stroma and grana stacks found in green algae and higher plants. While the photophysiology of diatoms has been studied extensively, very little is known about the spatial organization of the multimeric photosynthetic protein complexes within their thylakoid membranes. Here, using cryo-electron tomography, proteomics, and biophysical analyses, we elucidate the macromolecular composition, architecture, and spatial distribution of photosystem II complexes in diatom thylakoid membranes. Structural analyses reveal 2 distinct photosystem II populations: loose clusters of complexes associated with antenna proteins and compact 2D crystalline arrays of dimeric cores. Biophysical measurements reveal only 1 photosystem II functional absorption cross section, suggesting that only the former population is photosynthetically active. The tomographic data indicate that the arrays of photosystem II cores are physically separated from those associated with antenna proteins. We hypothesize that the islands of photosystem cores are repair stations, where photodamaged proteins can be replaced. Our results strongly imply convergent evolution between the red and the green photosynthetic lineages toward spatial segregation of dynamic, functional microdomains of photosystem II supercomplexes.
History
DepositionFeb 8, 2019-
Header (metadata) releaseFeb 20, 2019-
Map releaseAug 14, 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: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0539.png

Downloads & links

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Map

FileDownload / File: emd_0539.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAveraged structure of photosystem II holocomplex on thylakoid membrane from diatom
Voxel sizeX=Y=Z: 3.49 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.8863575 - 2.2579346
Average (Standard dev.)0.008281802 (±0.15222046)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 446.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.493.493.49
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z446.720446.720446.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.8862.2580.008

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Supplemental data

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Sample components

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Entire : Thylakoid membrane purified from diatom

EntireName: Thylakoid membrane purified from diatom
Components
  • Organelle or cellular component: Thylakoid membrane purified from diatom

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Supramolecule #1: Thylakoid membrane purified from diatom

SupramoleculeName: Thylakoid membrane purified from diatom / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Phaeodactylum tricornutum (Diatom) / Organelle: Thylakoid membrane

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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: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: LEICA EM GP
DetailsThylakoid membrane purified from diatom.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 2.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 173 / Number images used: 382 / Software - Name: EMAN2 (ver. 2.3)
CTF correctionSoftware - Name: EMAN2 (ver. 2.3)
Final 3D classificationNumber classes: 1 / Software - Name: EMAN2 (ver. 2.3)
Final angle assignmentType: OTHER / Software - Name: EMAN2 (ver. 2.3) / Details: subtomogram refinement
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.3) / Number subtomograms used: 382
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4yuu

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient

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