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- EMDB-62790: PSII-6 FCPII supercomplex from haptophyte Chrysotila roscoffensis -

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Basic information

Entry
Database: EMDB / ID: EMD-62790
TitlePSII-6 FCPII supercomplex from haptophyte Chrysotila roscoffensis
Map dataPSII-6 FCPII supercomplex from haptophyte Chrysotila roscoffensis.
Sample
  • Complex: Photosystem II (PSII)-fucoxanthin chlorophyll a/c binding protein II (FCPII) supercomplex from haptophyte Chrysotila roscoffensis
Keywordsphotosystem II / photosynthesis / chlorophyll / light-harvesting complex / energy transfer / LHCII / FCPII / coccolithophore / haptophyte
Biological speciesChrysotila roscoffensis (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsLa Rocca R / Kato K / Tsai P-C / Nakajima Y / Akita F / Shen J-R
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Structure of a photosystem II-FCPII supercomplex from a haptophyte reveals a distinct antenna organization.
Authors: Romain La Rocca / Koji Kato / Pi-Cheng Tsai / Yoshiki Nakajima / Fusamichi Akita / Jian-Ren Shen /
Abstract: Haptophytes are unicellular algae that produce 30 to 50% of biomass in oceans. Among haptophytes, a subset named coccolithophores is characterized by calcified scales. Despite the importance of ...Haptophytes are unicellular algae that produce 30 to 50% of biomass in oceans. Among haptophytes, a subset named coccolithophores is characterized by calcified scales. Despite the importance of coccolithophores in global carbon fixation and CaCO production, their energy conversion system is still poorly known. Here we report a cryo-electron microscopic structure of photosystem II (PSII)-fucoxanthin chlorophyll c-binding protein (FCPII) supercomplex from Chyrostila roscoffensis, a representative of coccolithophores. This complex has two sets of six dimeric and monomeric FCPIIs, with distinct orientations. Interfaces of both FCPII/FCPII and FCPII/core differ from previously reported. We also determine the sequence of Psb36, a subunit previously found in diatoms and red algae. The principal excitation energy transfer (EET) pathways involve mainly 5 FCPIIs, where one FCPII monomer mediates EET to CP47. Our findings provide a solid structural basis for EET and energy dissipation pathways occurring in coccolithophores.
History
DepositionDec 19, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62790.png

Downloads & links

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Map

FileDownload / File: emd_62790.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPSII-6 FCPII supercomplex from haptophyte Chrysotila roscoffensis.
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 600 pix.
= 436.2 Å		0.73 Å/pix.
x 600 pix.
= 436.2 Å		0.73 Å/pix.
x 600 pix.
= 436.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.25177038 - 0.45997614
Average (Standard dev.)0.00026761537 (±0.014441268)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 436.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A.

Fileemd_62790_half_map_1.map
AnnotationHalf map A.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B.

Fileemd_62790_half_map_2.map
AnnotationHalf map B.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Photosystem II (PSII)-fucoxanthin chlorophyll a/c binding protein...

EntireName: Photosystem II (PSII)-fucoxanthin chlorophyll a/c binding protein II (FCPII) supercomplex from haptophyte Chrysotila roscoffensis
Components
  • Complex: Photosystem II (PSII)-fucoxanthin chlorophyll a/c binding protein II (FCPII) supercomplex from haptophyte Chrysotila roscoffensis

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Supramolecule #1: Photosystem II (PSII)-fucoxanthin chlorophyll a/c binding protein...

SupramoleculeName: Photosystem II (PSII)-fucoxanthin chlorophyll a/c binding protein II (FCPII) supercomplex from haptophyte Chrysotila roscoffensis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #5-#11, #13-#15
Details: PSII-FCPII supercomplex containing two sets of 6 symmetrical FCPII.
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)

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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

Concentration1.53 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
50.0 mMNaClsodium chloride
0.05 %alpha-DDMn-Dodecyl alpha-maltoside
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: Light was turned off during the blot..

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 0.8 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio reconstruction
Final reconstructionNumber classes used: 12 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23837
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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