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- EMDB-72770: Composite Map of the Macrocystis pyrifera Photosystem I Supercomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-72770
TitleComposite Map of the Macrocystis pyrifera Photosystem I Supercomplex
Map data
Sample
  • Complex: Photosystem I from Macrocystis pyrifera
KeywordsPhotosystem I / Brown algae / Macrocystis pyrifera / PHOTOSYNTHESIS
Function / homology
Function and homology information


plastid thylakoid membrane / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding ...plastid thylakoid membrane / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily ...Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaA / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / : / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VIII / Photosystem I iron-sulfur center / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1
Similarity search - Component
Biological speciesMacrocystis pyrifera (giant kelp)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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: To Be Published
Title: Structure of a Photosystem-I-FCP supercomplex from brown alga Macrocystis pyrifera (giant kelp)
Authors: Weissman JD / Maturana P / Riddle R / Wyatt G / Dubinin VGT / Zerbe P / Maldonado M
History
DepositionSep 18, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72770.png

Downloads & links

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Map

FileDownload / File: emd_72770.map.gz / Format: CCP4 / Size: 15.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.22 Å/pix.
x 98 pix.
= 119.266 Å		1.22 Å/pix.
x 192 pix.
= 233.664 Å		1.22 Å/pix.
x 214 pix.
= 260.438 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-4.43045 - 7.046705
Average (Standard dev.)0.08050118 (±0.46661806)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions19221498
Spacing98192214
CellA: 119.266 Å / B: 233.664 Å / C: 260.438 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: GOLD / 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 133000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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