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- PDB-7ku5: The Structure of the moss PSI-LHCI reveals the evolution of the L... -

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Basic information

Entry
Database: PDB / ID: 7ku5
TitleThe Structure of the moss PSI-LHCI reveals the evolution of the LHCI antenna
ComponentsPsaO
KeywordsPHOTOSYNTHESIS / PSI / electron transport / chlorophyll / Antenna / light harvesting / membrane protein
Function / homologyPhotosystem I PsaO / PsaO transmembrane domain / membrane / BETA-CAROTENE / CHLOROPHYLL A / Photosystem I subunit O
Function and homology information
Biological speciesPhyscomitrium patens (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsRiddle, R. / Gorski, C. / Toporik, H. / Dobson, Z. / Da, Z. / Williams, D. / Mazor, Y.
Funding support1items
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, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
O: PsaO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9965
Polymers9,7781
Non-polymers3,2174
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein PsaO


Mass: 9778.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1JDE1
#2: Chemical ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PSI / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Physcomitrium patens (plant)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: RELION / Version: 3.1 / Category: final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15357 / Symmetry type: POINT

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