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- EMDB-35033: OutLHCIs plus Lhcb9 moiety of Large Photosystem I from Physcomitr... -

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Basic information

Entry
Database: EMDB / ID: EMD-35033
TitleOutLHCIs plus Lhcb9 moiety of Large Photosystem I from Physcomitrium patens
Map dataFocused refinement map of the outLHCIs plus Lhcb9 moiety of PpPSI-L
Sample
  • Complex: Outer LHCIs plus Lhcb9 moiety of Large Photosystem I from Physcomitrium patens
KeywordsPhotosystem I / Lhcb9 / PHOTOSYNTHESIS
Biological speciesPhyscomitrium patens (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsSun HY / Li M / Pan XW
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970264 China
National Natural Science Foundation of China (NSFC)31930064 China
Chinese Academy of SciencesXDB27020106 China
Chinese Academy of SciencesXDB37020101 China
CitationJournal: Nat Plants / Year: 2023
Title: Structural insights into the assembly and energy transfer of the Lhcb9-dependent photosystem I from moss Physcomitrium patens.
Authors: Haiyu Sun / Hui Shang / Xiaowei Pan / Mei Li /
Abstract: In plants and green algae, light-harvesting complexes I and II (LHCI and LHCII) constitute the antennae of photosystem I (PSI), thus effectively increasing the cross-section of the PSI core. The moss ...In plants and green algae, light-harvesting complexes I and II (LHCI and LHCII) constitute the antennae of photosystem I (PSI), thus effectively increasing the cross-section of the PSI core. The moss Physcomitrium patens (P. patens) represents a well-studied primary land-dwelling photosynthetic autotroph branching from the common ancestor of green algae and land plants at the early stage of evolution. P. patens possesses at least three types of PSI with different antenna sizes. The largest PSI form (PpPSI-L) exhibits a unique organization found neither in flowering plants nor in algae. Its formation is mediated by the P. patens-specific LHC protein, Lhcb9. While previous studies have revealed the overall architecture of PpPSI-L, its assembly details and the relationship between different PpPSI types remain unclear. Here we report the high-resolution structure of PpPSI-L. We identified 14 PSI core subunits, one Lhcb9, one phosphorylated LHCII trimer and eight LHCI monomers arranged as two belts. Our structural analysis established the essential role of Lhcb9 and the phosphorylated LHCII in stabilizing the complex. In addition, our results suggest that PpPSI switches between different types, which share identical modules. This feature may contribute to the dynamic adjustment of the light-harvesting capability of PSI under different light conditions.
History
DepositionDec 23, 2022-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateAug 2, 2023-
Current statusAug 2, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35033.png

Downloads & links

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Map

FileDownload / File: emd_35033.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement map of the outLHCIs plus Lhcb9 moiety of PpPSI-L
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.0148
Minimum - Maximum-0.107445724 - 0.1502041
Average (Standard dev.)0.00002146884 (±0.0019719664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35033_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35033_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Outer LHCIs plus Lhcb9 moiety of Large Photosystem I from Physcom...

EntireName: Outer LHCIs plus Lhcb9 moiety of Large Photosystem I from Physcomitrium patens
Components
  • Complex: Outer LHCIs plus Lhcb9 moiety of Large Photosystem I from Physcomitrium patens

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Supramolecule #1: Outer LHCIs plus Lhcb9 moiety of Large Photosystem I from Physcom...

SupramoleculeName: Outer LHCIs plus Lhcb9 moiety of Large Photosystem I from Physcomitrium patens
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Physcomitrium patens (plant)

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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: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
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:

7d0j


Details: 7KSQ
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 89945

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