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- EMDB-31243: Cryo-electron tomography of phycobilisome-photosystem II supercom... -

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Basic information

Entry
Database: EMDB / ID: EMD-31243
TitleCryo-electron tomography of phycobilisome-photosystem II supercomplex on the thylakoid
Map data
Sample
  • Cell: phycobilisome-photosystem II supercomplex
Biological speciesPorphyridium purpureum (eukaryote)
Methodelectron tomography / cryo EM
AuthorsSui SF / Li XM / Li MJ / Ma JF
Funding support China, 4 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFA0504600 China
National Basic Research Program of China (973 Program)2016YFA0501902 China
National Basic Research Program of China (973 Program)31861143048 China
National Basic Research Program of China (973 Program)31722015 China
CitationJournal: Elife / Year: 2021
Title: In situ cryo-ET structure of phycobilisome-photosystem II supercomplex from red alga.
Authors: Meijing Li / Jianfei Ma / Xueming Li / Sen-Fang Sui /
Abstract: Phycobilisome (PBS) is the main light-harvesting antenna in cyanobacteria and red algae. How PBS transfers the light energy to photosystem II (PSII) remains to be elucidated. Here we report the in ...Phycobilisome (PBS) is the main light-harvesting antenna in cyanobacteria and red algae. How PBS transfers the light energy to photosystem II (PSII) remains to be elucidated. Here we report the in situ structure of the PBS-PSII supercomplex from UTEX 2757 using cryo-electron tomography and subtomogram averaging. Our work reveals the organized network of hemiellipsoidal PBS with PSII on the thylakoid membrane in the native cellular environment. In the PBS-PSII supercomplex, each PBS interacts with six PSII monomers, of which four directly bind to the PBS, and two bind indirectly. Additional three 'connector' proteins also contribute to the connections between PBS and PSIIs. Two PsbO subunits from adjacent PSII dimers bind with each other, which may promote stabilization of the PBS-PSII supercomplex. By analyzing the interaction interface between PBS and PSII, we reveal that α and ApcD connect with CP43 of PSII monomer and that α also interacts with CP47' of the neighboring PSII monomer, suggesting the multiple light energy delivery pathways. The in situ structures illustrate the coupling pattern of PBS and PSII and the arrangement of the PBS-PSII supercomplex on the thylakoid, providing the near-native 3D structural information of the various energy transfer from PBS to PSII.
History
DepositionApr 26, 2021-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateMar 2, 2022-
Current statusMar 2, 2022Processing site: PDBj / Status: Released

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Structure visualization

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

emd_31243.png

Downloads & links

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Map

FileDownload / File: emd_31243.map.gz / Format: CCP4 / Size: 308.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 13.684 Å
Density
Minimum - Maximum-0.3847499 - 0.81049097
Average (Standard dev.)0.22692887 (±0.09188617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-281
Dimensions92795991
Spacing95992791
CellA: 13122.956 Å / B: 12685.068 Å / C: 1245.244 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z13.68413.68413.684
M x/y/z95992791
origin x/y/z0.0000.0000.000
length x/y/z13122.95612685.0681245.244
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS00-281
NC/NR/NS95992791
D min/max/mean-0.3850.8100.227

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Supplemental data

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Sample components

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Entire : phycobilisome-photosystem II supercomplex

EntireName: phycobilisome-photosystem II supercomplex
Components
  • Cell: phycobilisome-photosystem II supercomplex

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Supramolecule #1: phycobilisome-photosystem II supercomplex

SupramoleculeName: phycobilisome-photosystem II supercomplex / type: cell / ID: 1 / Parent: 0 / Details: phycobilisome, photosystem II
Source (natural)Organism: Porphyridium purpureum (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.1 nA / Focused ion beam - Duration: 3600 sec. / Focused ion beam - Temperature: 191 K / Focused ion beam - Initial thickness: 1000 nm / Focused ion beam - Final thickness: 200 nm
Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Quanta FIB. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 120.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Number images used: 51

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Atomic model buiding 1

Initial model(PDB ID:

6kgx

,

4yuu

)
RefinementProtocol: FLEXIBLE FIT

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