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- EMDB-60827: The consensus map of TEF30-associated C2S-type PSII supercomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-60827
TitleThe consensus map of TEF30-associated C2S-type PSII supercomplex
Map data
Sample
  • Complex: TEF30-associated C2S-type PSII-LHCII supercomplex
Keywordsphotosystem II / PSII repair / PSII assembly / PSII intermediate / TEF30 / C2S / supercomplex / PHOTOSYNTHESIS
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsWang Y / Liu Z
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Plants / Year: 2025
Title: Roles of multiple TEF30-associated intermediate complexes in the repair and reassembly of photosystem II in Chlamydomonas reinhardtii.
Authors: Yidi Wang / Chenxi Wang / Anjie Li / Zhenfeng Liu /
Abstract: During oxygenic photosynthesis, photosystem II (PSII) uses light energy for oxidizing water and reducing plastoquinone. It is susceptible to photodamage, and the damaged PSII is repaired through a ...During oxygenic photosynthesis, photosystem II (PSII) uses light energy for oxidizing water and reducing plastoquinone. It is susceptible to photodamage, and the damaged PSII is repaired through a sophisticated biological process assisted by numerous auxiliary proteins. Here we report the cryogenic electron microscopy structures of four PSII-repair complexes from Chlamydomonas reinhardtii associated with the Thylakoid Enriched Fraction 30 (TEF30, an orthologue of plant MET1) protein-namely, a TEF30-PSII core monomer (TEF30-C), two types of TEF30-PSII core dimers (types I and II, TEF30-C-I and TEF30-C-II) and a TEF30-CS-type PSII-LHCII supercomplex (TEF30-CS; S, strongly associated light-harvesting complex II trimer). TEF30 mediates the assembly of CP43 with the RC47 module by clamping on the stromal surfaces and prevents the premature association of peripheral antennae with PSII-C. In the transition from TEF30-C-I to TEF30-C-II, TEF30-CS and mature CS, one PSII core slides along the dimerization interface against the adjacent one by 22-35 Å, generating a zigzagged surface for accommodating the peripheral antennae. These results suggest that the PSII repair process undergoes multiple TEF30-mediated intermediate states to form intact PSII-LHCII supercomplexes.
History
DepositionJul 16, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60827.png

Downloads & links

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Map

FileDownload / File: emd_60827.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.50337976 - 0.9148049
Average (Standard dev.)0.00015321514 (±0.03254421)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60827_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_60827_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 : TEF30-associated C2S-type PSII-LHCII supercomplex

EntireName: TEF30-associated C2S-type PSII-LHCII supercomplex
Components
  • Complex: TEF30-associated C2S-type PSII-LHCII supercomplex

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Supramolecule #1: TEF30-associated C2S-type PSII-LHCII supercomplex

SupramoleculeName: TEF30-associated C2S-type PSII-LHCII supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#33
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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6kac

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24832
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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