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- EMDB-37289: A focused cryo-EM map of an intermediate-state complex during the... -

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Basic information

Entry
Database: EMDB / ID: EMD-37289
TitleA focused cryo-EM map of an intermediate-state complex during the process of photosystem II repair (Part 2)
Map data
Sample
  • Complex: An intermidiate complex of the PSII-repair cycle containing PSII-M and PRF2
KeywordsPhotosystem II repair / PSII core monomer / PHOTOSYNTHESIS
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsLi A / Wang Y / Liu Z
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31925024 China
Chinese Academy of SciencesYSBR-015 China
Chinese Academy of SciencesXDB37020101 China
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for an early stage of the photosystem II repair cycle in Chlamydomonas reinhardtii.
Authors: Anjie Li / Tingting You / Xiaojie Pang / Yidi Wang / Lijin Tian / Xiaobo Li / Zhenfeng Liu /
Abstract: Photosystem II (PSII) catalyzes water oxidation and plastoquinone reduction by utilizing light energy. It is highly susceptible to photodamage under high-light conditions and the damaged PSII needs ...Photosystem II (PSII) catalyzes water oxidation and plastoquinone reduction by utilizing light energy. It is highly susceptible to photodamage under high-light conditions and the damaged PSII needs to be restored through a process known as the PSII repair cycle. The detailed molecular mechanism underlying the PSII repair process remains mostly elusive. Here, we report biochemical and structural features of a PSII-repair intermediate complex, likely arrested at an early stage of the PSII repair process in the green alga Chlamydomonas reinhardtii. The complex contains three protein factors associated with a damaged PSII core, namely Thylakoid Enriched Factor 14 (TEF14), Photosystem II Repair Factor 1 (PRF1), and Photosystem II Repair Factor 2 (PRF2). TEF14, PRF1 and PRF2 may facilitate the release of the manganese-stabilizing protein PsbO, disassembly of peripheral light-harvesting complexes from PSII and blockage of the Q site, respectively. Moreover, an α-tocopherol quinone molecule is located adjacent to the heme group of cytochrome b, potentially fulfilling a photoprotective role by preventing the generation of reactive oxygen species.
History
DepositionAug 26, 2023-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37289.png

Downloads & links

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Map

FileDownload / File: emd_37289.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 320 pix.
= 332.8 Å		1.04 Å/pix.
x 320 pix.
= 332.8 Å		1.04 Å/pix.
x 320 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.0011711209 - 0.1193715
Average (Standard dev.)-0.0000011465595 (±0.0017496636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37289_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37289_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : An intermidiate complex of the PSII-repair cycle containing PSII-...

EntireName: An intermidiate complex of the PSII-repair cycle containing PSII-M and PRF2
Components
  • Complex: An intermidiate complex of the PSII-repair cycle containing PSII-M and PRF2

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Supramolecule #1: An intermidiate complex of the PSII-repair cycle containing PSII-...

SupramoleculeName: An intermidiate complex of the PSII-repair cycle containing PSII-M and PRF2
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 397491
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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