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- EMDB-14872: Plastocyanin bound to PSI of Chlamydomonas reinhardtii -

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Basic information

Entry
Database: EMDB / ID: EMD-14872
TitlePlastocyanin bound to PSI of Chlamydomonas reinhardtii
Map data
Sample
  • Organelle or cellular component: Photosystem I dimer of Chlamydomonas reinhardtii
    • Protein or peptide: Plastocyanin, chloroplastic
  • Ligand: COPPER (II) ION
KeywordsPhotosynthesis / green algae / dimeric PSI
Function / homology
Function and homology information


chloroplast thylakoid membrane / electron transfer activity / copper ion binding
Similarity search - Function
Plastocyanin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxin
Similarity search - Domain/homology
Plastocyanin, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsNaschberger A / Amunts A
Funding support Sweden, Germany, 4 items
OrganizationGrant numberCountry
The Swedish Foundation for Strategic ResearchARC19-0051 Sweden
Knut and Alice Wallenberg Foundation2018.0080 Sweden
German Federal Ministry for Education and ResearchNRW 28 313-WO44A Germany
German-Israeli Foundation for Research and DevelopmentG-1483- 207/2018 Germany
CitationJournal: Nat Plants / Year: 2022
Title: Algal photosystem I dimer and high-resolution model of PSI-plastocyanin complex.
Authors: Andreas Naschberger / Laura Mosebach / Victor Tobiasson / Sebastian Kuhlgert / Martin Scholz / Annemarie Perez-Boerema / Thi Thu Hoai Ho / André Vidal-Meireles / Yuichiro Takahashi / ...Authors: Andreas Naschberger / Laura Mosebach / Victor Tobiasson / Sebastian Kuhlgert / Martin Scholz / Annemarie Perez-Boerema / Thi Thu Hoai Ho / André Vidal-Meireles / Yuichiro Takahashi / Michael Hippler / Alexey Amunts /
Abstract: Photosystem I (PSI) enables photo-electron transfer and regulates photosynthesis in the bioenergetic membranes of cyanobacteria and chloroplasts. Being a multi-subunit complex, its macromolecular ...Photosystem I (PSI) enables photo-electron transfer and regulates photosynthesis in the bioenergetic membranes of cyanobacteria and chloroplasts. Being a multi-subunit complex, its macromolecular organization affects the dynamics of photosynthetic membranes. Here we reveal a chloroplast PSI from the green alga Chlamydomonas reinhardtii that is organized as a homodimer, comprising 40 protein subunits with 118 transmembrane helices that provide scaffold for 568 pigments. Cryogenic electron microscopy identified that the absence of PsaH and Lhca2 gives rise to a head-to-head relative orientation of the PSI-light-harvesting complex I monomers in a way that is essentially different from the oligomer formation in cyanobacteria. The light-harvesting protein Lhca9 is the key element for mediating this dimerization. The interface between the monomers is lacking PsaH and thus partially overlaps with the surface area that would bind one of the light-harvesting complex II complexes in state transitions. We also define the most accurate available PSI-light-harvesting complex I model at 2.3 Å resolution, including a flexibly bound electron donor plastocyanin, and assign correct identities and orientations to all the pigments, as well as 621 water molecules that affect energy transfer pathways.
History
DepositionApr 29, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14872.png

Downloads & links

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Map

FileDownload / File: emd_14872.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 700 pix.
= 588. Å		0.84 Å/pix.
x 700 pix.
= 588. Å		0.84 Å/pix.
x 700 pix.
= 588. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.022918815 - 0.0515673
Average (Standard dev.)0.000008410725 (±0.00042390914)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 588.0 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 dimer of Chlamydomonas reinhardtii

EntireName: Photosystem I dimer of Chlamydomonas reinhardtii
Components
  • Organelle or cellular component: Photosystem I dimer of Chlamydomonas reinhardtii
    • Protein or peptide: Plastocyanin, chloroplastic
  • Ligand: COPPER (II) ION

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Supramolecule #1: Photosystem I dimer of Chlamydomonas reinhardtii

SupramoleculeName: Photosystem I dimer of Chlamydomonas reinhardtii / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 700 KDa

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Macromolecule #1: Plastocyanin, chloroplastic

MacromoleculeName: Plastocyanin, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 14.889784 KDa
SequenceString:
MKATLRAPAS RASAVRPVAS LKAAAQRVAS VAGVSVASLA LTLAAHADAT VKLGADSGAL EFVPKTLTIK SGETVNFVNN AGFPHNIVF DEDAIPSGVN ADAISRDDYL NAPGETYSVK LTAAGEYGYY CEPHQGAGMV GKIIVQ

UniProtKB: Plastocyanin, chloroplastic

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Macromolecule #2: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66080
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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