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- EMDB-76146: Composite map of Macrocystis pyrifera PSI-FCP supercomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-76146
TitleComposite map of Macrocystis pyrifera PSI-FCP supercomplex
Map dataComposite map of Macrocystis pyrifera photosystem I - FCP supercomplex. Local resolution ranging from 2.47 to 5.21 A.
Sample
  • Complex: Photosystem I from Macrocystis pyrifera
KeywordsPhotosystem I / Brown algae / Macrocystis pyrifera / PHOTOSYNTHESIS
Biological speciesMacrocystis pyrifera (giant kelp)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsMaturana P / Maldonado M
Funding support United States, 2 items
OrganizationGrant numberCountry
Other privateUCD Hellman Foundation United States
Other governmentS2C2 C-S2C-ST-CA237 United States
CitationJournal: Nat Commun / Year: 2026
Title: Structure of giant kelp Photosystem I-FCP uncovers drivers of antenna evolution across the red lineage.
Authors: Jenevieve D Weissman / Pablo Maturana / Hui M O Oung / Reece Riddle / Gabrielle Wyatt / Viktoria G T Dubinin / Philipp Zerbe / María Maldonado /
Abstract: Brown algae and other red-algae-derived organisms are major contributors to global CO fixation via photosynthesis. To understand the photosynthetic function of brown algae, we obtained the structure ...Brown algae and other red-algae-derived organisms are major contributors to global CO fixation via photosynthesis. To understand the photosynthetic function of brown algae, we obtained the structure of giant kelp Macrocystis pyrifera photosystem I (PSI) with a fucoxanthin-chlorophyll-protein (FCP) antenna and compared it to known structures from the red-algal lineage. We identified differences in M. pyrifera's antenna composition, architecture, and chlorophyll networks, as well as a pronounced variation in transmembrane hydrophobic thickness across the PSI-FCP supercomplex, with implications for photochemical function. Our work lays the foundation to understand kelp's high photosynthetic productivity and reveals drivers of antenna conservation and diversification for the red lineage.
History
DepositionMar 16, 2026-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76146.png

Downloads & links

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Map

FileDownload / File: emd_76146.map.gz / Format: CCP4 / Size: 14.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of Macrocystis pyrifera photosystem I - FCP supercomplex. Local resolution ranging from 2.47 to 5.21 A.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.22 Å/pix.
x 95 pix.
= 115.615 Å		1.22 Å/pix.
x 184 pix.
= 223.928 Å		1.22 Å/pix.
x 212 pix.
= 258.004 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.217 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-3.920826 - 6.4736104
Average (Standard dev.)0.08357601 (±0.4433441)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions18421295
Spacing95184212
CellA: 115.615 Å / B: 223.92801 Å / C: 258.004 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Photosystem I from Macrocystis pyrifera

EntireName: Photosystem I from Macrocystis pyrifera
Components
  • Complex: Photosystem I from Macrocystis pyrifera

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Supramolecule #1: Photosystem I from Macrocystis pyrifera

SupramoleculeName: Photosystem I from Macrocystis pyrifera / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Macrocystis pyrifera (giant kelp)

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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: 7.5
Component:
ConcentrationFormulaName
15.0 mMHEPESHEPES
20.0 mMKClPotassium chloride
5.0 mMNaClSodium chloride
0.01 w/vC56H92O25GDN
0.1 w/vDigitoninDigitonin
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 20
VitrificationCryogen name: ETHANE / Chamber humidity: 90 %
Details1 mg/mL of Chl

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 15690 / Average exposure time: 4.95 sec. / 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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1)
Details: Composite cryo-EM map of the Macrocystis pyrifera photosystem I-FCP supercomplex generated by merging locally refined reconstructions. The global resolution is 2.47 A based on the FSC 0.143 ...Details: Composite cryo-EM map of the Macrocystis pyrifera photosystem I-FCP supercomplex generated by merging locally refined reconstructions. The global resolution is 2.47 A based on the FSC 0.143 criterion, with local resolution ranging from 2.47 to 5.21 A.
Number images used: 133000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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