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- EMDB-6930: Cryo-EM structure of the red algal PSI-LHCR -

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Basic information

Entry
Database: EMDB / ID: EMD-6930
TitleCryo-EM structure of the red algal PSI-LHCR
Map data
Sample
  • Complex: PSI-5Lhcr
Function / homology
Function and homology information


thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / thylakoid / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane ...thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / thylakoid / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I PsaO / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI ...Photosystem I PsaO / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / 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 PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaA / 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
Similar to chlorophyll a/b-binding protein, CP24 / Photosystem I subunit O / Similar to light harvesting protein / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 ...Similar to chlorophyll a/b-binding protein, CP24 / Photosystem I subunit O / Similar to light harvesting protein / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I iron-sulfur center subunit VII / Photosystem I iron-sulfur center / PSI-K / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesCyanidioschyzon merolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsPi X
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Unique organization of photosystem I-light-harvesting supercomplex revealed by cryo-EM from a red alga.
Authors: Xiong Pi / Lirong Tian / Huai-En Dai / Xiaochun Qin / Lingpeng Cheng / Tingyun Kuang / Sen-Fang Sui / Jian-Ren Shen /
Abstract: Photosystem I (PSI) is one of the two photosystems present in oxygenic photosynthetic organisms and functions to harvest and convert light energy into chemical energy in photosynthesis. In eukaryotic ...Photosystem I (PSI) is one of the two photosystems present in oxygenic photosynthetic organisms and functions to harvest and convert light energy into chemical energy in photosynthesis. In eukaryotic algae and higher plants, PSI consists of a core surrounded by variable species and numbers of light-harvesting complex (LHC)I proteins, forming a PSI-LHCI supercomplex. Here, we report cryo-EM structures of PSI-LHCR from the red alga in two forms, one with three Lhcr subunits attached to the side, similar to that of higher plants, and the other with two additional Lhcr subunits attached to the opposite side, indicating an ancient form of PSI-LHCI. Furthermore, the red algal PSI core showed features of both cyanobacterial and higher plant PSI, suggesting an intermediate type during evolution from prokaryotes to eukaryotes. The structure of PsaO, existing in eukaryotic organisms, was identified in the PSI core and binds three chlorophylls and may be important in harvesting energy and in mediating energy transfer from LHCII to the PSI core under state-2 conditions. Individual attaching sites of LHCRs with the core subunits were identified, and each Lhcr was found to contain 11 to 13 chlorophylls and 5 zeaxanthins, which are apparently different from those of LHCs in plant PSI-LHCI. Together, our results reveal unique energy transfer pathways different from those of higher plant PSI-LHCI, its adaptation to the changing environment, and the possible changes of PSI-LHCI during evolution from prokaryotes to eukaryotes.
History
DepositionMar 8, 2018-
Header (metadata) releaseApr 11, 2018-
Map releaseApr 11, 2018-
UpdateJan 22, 2020-
Current statusJan 22, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.087
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.087
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5zgh
  • Surface level: 0.087
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6930.png

Downloads & links

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Map

FileDownload / File: emd_6930.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.087 / Movie #1: 0.087
Minimum - Maximum-0.16069043 - 0.5837396
Average (Standard dev.)-0.00004356571 (±0.014275645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 294.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z294.000294.000294.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1610.584-0.000

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Supplemental data

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Sample components

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Entire : PSI-5Lhcr

EntireName: PSI-5Lhcr
Components
  • Complex: PSI-5Lhcr

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Supramolecule #1: PSI-5Lhcr

SupramoleculeName: PSI-5Lhcr / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Cyanidioschyzon merolae (eukaryote)

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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

Concentration3.0 mg/mL
BufferpH: 7.4
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 2.17 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:

4xk8

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 124279

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