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- EMDB-23034: The Structure of the moss PSI-LHCI reveals the evolution of the L... -

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Basic information

Entry
Database: EMDB / ID: EMD-23034
TitleThe Structure of the moss PSI-LHCI reveals the evolution of the LHCI antenna
Map data
Sample
  • Complex: PSI
    • Protein or peptide: PsaO
  • Ligand: CHLOROPHYLL A
  • Ligand: BETA-CAROTENE
KeywordsPSI / electron transport / photosynthesis / chlorophyll / Antenna / light harvesting / membrane protein
Function / homologyPhotosystem I PsaO / PsaO transmembrane domain / membrane / Photosystem I subunit O
Function and homology information
Biological speciesPhyscomitrium patens (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsRiddle R / Gorski C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Plants / Year: 2022
Title: The structure of the Physcomitrium patens photosystem I reveals a unique Lhca2 paralogue replacing Lhca4.
Authors: C Gorski / R Riddle / H Toporik / Z Da / Z Dobson / D Williams / Y Mazor /
Abstract: The moss Physcomitrium patens diverged from green algae shortly after the colonization of land by ancient plants. This colonization posed new environmental challenges, which drove evolutionary ...The moss Physcomitrium patens diverged from green algae shortly after the colonization of land by ancient plants. This colonization posed new environmental challenges, which drove evolutionary processes. The photosynthetic machinery of modern flowering plants is adapted to the high light conditions on land. Red-shifted Lhca4 antennae are present in the photosystem I light-harvesting complex of many green-lineage plants but absent in P. patens. The cryo-EM structure of the P. patens photosystem I light-harvesting complex I supercomplex (PSI-LHCI) at 2.8 Å reveals that Lhca4 is replaced by a unique Lhca2 paralogue in moss. This PSI-LHCI supercomplex also retains the PsaM subunit, present in Cyanobacteria and several algal species but lost in vascular plants, and the PsaO subunit responsible for binding light-harvesting complex II. The blue-shifted Lhca2 paralogue and chlorophyll b enrichment relative to flowering plants make the P. patens PSI-LHCI spectroscopically unique among other green-lineage supercomplexes. Overall, the structure represents an evolutionary intermediate PSI with the crescent-shaped LHCI common in vascular plants, and contains a unique Lhca2 paralogue that facilitates the moss's adaptation to low-light niches.
History
DepositionNov 24, 2020-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_23034.png

Downloads & links

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Map

FileDownload / File: emd_23034.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 280 pix.
= 291.2 Å		1.04 Å/pix.
x 280 pix.
= 291.2 Å		1.04 Å/pix.
x 280 pix.
= 291.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-6.4320965 - 8.676752
Average (Standard dev.)-0.000000000044737 (±0.15294826)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 291.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : PSI

EntireName: PSI
Components
  • Complex: PSI
    • Protein or peptide: PsaO
  • Ligand: CHLOROPHYLL A
  • Ligand: BETA-CAROTENE

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Supramolecule #1: PSI

SupramoleculeName: PSI / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Physcomitrium patens (plant)

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Macromolecule #1: PsaO

MacromoleculeName: PsaO / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 9.778286 KDa
SequenceString:
NRDWLRRDLS VIGFGLIGWL APSSLPVING NSLTGLFLGS IGPELAHFPT GPALTSPFWL WMVTWHVGLF IVLTFGQIGF KGRQDGYW

UniProtKB: Photosystem I subunit O

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Macromolecule #2: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 2 / Number of copies: 3 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #3: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 3 / Number of copies: 1 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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

5l8r

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15357
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)

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