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- EMDB-38913: Focus refinement map of PSII-CAC -

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Basic information

Entry
Database: EMDB / ID: EMD-38913
TitleFocus refinement map of PSII-CAC
Map dataFocus refinement map of 6CAC of PSII-CAC from Rhodomonas salina
Sample
  • Complex: Inactive Photosystem II associated with chlorophyll a/c binding protein
    • Other: CAC antenna
KeywordsPhotosystem II associated with CAC antenna from Rhodomonas Salina / PHOTOSYNTHESIS
Biological speciesRhodomonas salina (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSi L / Li M
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program) China
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for the distinct core-antenna assembly of cryptophyte photosystem II.
Authors: Long Si / Shumeng Zhang / Xiaodong Su / Mei Li /
Abstract: Photosystem II (PSII) catalyzes the light-driven charge separation and water oxidation reactions of photosynthesis. Eukaryotic PSII core is usually associated with membrane-embedded light-harvesting ...Photosystem II (PSII) catalyzes the light-driven charge separation and water oxidation reactions of photosynthesis. Eukaryotic PSII core is usually associated with membrane-embedded light-harvesting antennae, which greatly increase the absorbance cross-section of the core. The peripheral antennae in different phototrophs vary considerably in protein composition and arrangement. Photosynthetic cryptophytes possess chlorophyll a/c binding proteins (CACs) that serve as their antennae. How these CACs assemble with the PSII core remains unclear. Here, we report the 2.57-Å resolution structure of cryptophyte PSII-CAC purified from cells at nitrogen-limited stationary growth phase. We show that each monomer of the PSII homodimer contains a core complex, six chlorophyll a/c binding proteins (CACs) and a previously unseen chlorophyll-binding protein (termed CAL-II). Six CACs are arranged as a double-layered arc-shaped non-parallel belt, and two such belts attach to the dimeric core from opposite sides. The CAL-II simultaneously interacts with a number of core subunits and five CACs. The distinct organization of CACs and the presence of CAL-II may play a critical role in stabilizing the dimeric PSII-CAC complex under stress conditions. Our study provides mechanistic insights into the assembly and function of the PSII-CAC complex as well as the possible adaptation of cryptophytes in response to environmental stresses.
History
DepositionJan 30, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38913.png

Downloads & links

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Map

FileDownload / File: emd_38913.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocus refinement map of 6CAC of PSII-CAC from Rhodomonas salina
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 416 pix.
= 432.653 Å		1.04 Å/pix.
x 416 pix.
= 432.653 Å		1.04 Å/pix.
x 416 pix.
= 432.653 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04003 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0239
Minimum - Maximum-0.07745012 - 0.17350091
Average (Standard dev.)0.0000544882 (±0.001706374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 432.65326 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38913_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_38913_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 : Inactive Photosystem II associated with chlorophyll a/c binding p...

EntireName: Inactive Photosystem II associated with chlorophyll a/c binding protein
Components
  • Complex: Inactive Photosystem II associated with chlorophyll a/c binding protein
    • Other: CAC antenna

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Supramolecule #1: Inactive Photosystem II associated with chlorophyll a/c binding p...

SupramoleculeName: Inactive Photosystem II associated with chlorophyll a/c binding protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rhodomonas salina (eukaryote)

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Macromolecule #1: CAC antenna

MacromoleculeName: CAC antenna / type: other / ID: 1 / Classification: other
Source (natural)Organism: Rhodomonas salina (eukaryote)
SequenceString:
NO

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: DIRECT ELECTRON DE-16 (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: 2.2 µm / Nominal defocus min: 1.2 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6jlu

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 123227
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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