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- EMDB-54455: Cryo-EM structure of Posidonia oceanica PSI-LHCI supercomplex - C... -

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Basic information

Entry
Database: EMDB / ID: EMD-54455
TitleCryo-EM structure of Posidonia oceanica PSI-LHCI supercomplex - Composite map
Map datacomposite map
Sample
  • Complex: Photosystem I (PSI-LHCI)
    • Protein or peptide: x 16 types
  • Ligand: x 11 types
KeywordsPhotosystem I / PSI-LHCI / Posidonia oceanica / Photosynthesis
Biological speciesPosidonia oceanica (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsCapaldi S / Amelii A / Sanita G / Esposito M / Bassi R
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101053983-GrInSunEuropean Union
CitationJournal: Nat Commun / Year: 2026
Title: Structural and spectral adaptation of the seagrass Posidonia oceanica photosystem I to seabed light.
Authors: Antonello Amelii / Stefano Capaldi / Mattia Russo / Zeno Guardini / Gennaro Sanità / Emanuela Esposito / Irene Olivé / Margherita Maiuri / Luca Dall'Osto / Giulio Cerullo / Gabriele ...Authors: Antonello Amelii / Stefano Capaldi / Mattia Russo / Zeno Guardini / Gennaro Sanità / Emanuela Esposito / Irene Olivé / Margherita Maiuri / Luca Dall'Osto / Giulio Cerullo / Gabriele Procaccini / Roberto Bassi /
Abstract: Seagrasses are marine angiosperms re-adapted to underwater life, forming productive ecosystems and long-term carbon sinks. Posidonia oceanica thrives up to 50 m depth, where light is scarce and ...Seagrasses are marine angiosperms re-adapted to underwater life, forming productive ecosystems and long-term carbon sinks. Posidonia oceanica thrives up to 50 m depth, where light is scarce and spectrally shifted; yet, the molecular basis of its photosynthetic adaptation remains unclear. Here, we report that P. oceanica genetically adapts for highly efficient photon use under dim light by enhancing photosystem antenna size and reducing exciton trapping time. We determine the structures of P. oceanica PSI supercomplexes by cryo-electron microscopy, revealing an expanded antenna system composed of PSI-LHCI, a trimeric phospho-LHCII, and an additional LHCI heterodimer. Low-energy chlorophyll forms associated with LHCI are lost. Ultrafast spectroscopy shows that this loss correlates with faster exciton trapping, which compensates for antenna expansion and enhances light-use efficiency under dim light. We identify key residues responsible for the loss of low-energy forms. Reversion to land-plant ortholog sequences restores red-shifted emission, providing strategies to enhance light-use efficiency in crops.
History
DepositionJul 18, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54455.png

Downloads & links

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Map

FileDownload / File: emd_54455.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.92 Å/pix.
x 400 pix.
= 368. Å		0.92 Å/pix.
x 400 pix.
= 368. Å		0.92 Å/pix.
x 400 pix.
= 368. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.3
Minimum - Maximum-19.686316999999999 - 40.985934999999998
Average (Standard dev.)0.0019309204 (±0.9859702)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 368.0 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 (PSI-LHCI)

EntireName: Photosystem I (PSI-LHCI)
Components
  • Complex: Photosystem I (PSI-LHCI)
    • Protein or peptide: Chlorophyll a-b binding protein 6, chloroplastic (Lhca1)
    • Protein or peptide: Photosystem I chlorophyll a/b-binding protein 2 (Lhca2)
    • Protein or peptide: Photosystem I chlorophyll a/b-binding protein 3-1 (Lhca3)
    • Protein or peptide: Chlorophyll a-b binding protein 4 (Lhca4)
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1 (PsaA)
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2 (PsaB)
    • Protein or peptide: Photosystem I iron-sulfur center (PsaC)
    • Protein or peptide: Photosystem I reaction center subunit II-1 (PsaD)
    • Protein or peptide: Photosystem I reaction center subunit IV A (PsaE1)
    • Protein or peptide: Photosystem I reaction center subunit III (PsaF)
    • Protein or peptide: Photosystem I reaction center subunit V (PsaG)
    • Protein or peptide: Photosystem I reaction center subunit VI-1 (PsaH1)
    • Protein or peptide: Photosystem I reaction center subunit VIII (PsaI)
    • Protein or peptide: Photosystem I reaction center subunit IX (PsaJ)
    • Protein or peptide: Photosystem I reaction center subunit psaK (PsaK)
    • Protein or peptide: Photosystem I reaction center subunit XI (PsaL)
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Supramolecule #1: Photosystem I (PSI-LHCI)

SupramoleculeName: Photosystem I (PSI-LHCI) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Posidonia oceanica (plant)

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Macromolecule #1: Chlorophyll a-b binding protein 6, chloroplastic (Lhca1)

MacromoleculeName: Chlorophyll a-b binding protein 6, chloroplastic (Lhca1)
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Posidonia oceanica (plant)
Molecular weightTheoretical: 21.878111 KDa
SequenceString: SAEWMPGQPR PPYLDGSAPG DFGFDPLRLG EVPSNLERFK EAELIHCRWA MLAVPGILVP EALGLGNWVK AQEWAAVPGG QATYLGNPV PWGTLPIILA VEFITIAFAE QLRSMEKDPE KKKYPGGAFD PLGFSKDPAK LQEFKVKEIK NGRLALLAFV G FCVQQSAY ...String:
SAEWMPGQPR PPYLDGSAPG DFGFDPLRLG EVPSNLERFK EAELIHCRWA MLAVPGILVP EALGLGNWVK AQEWAAVPGG QATYLGNPV PWGTLPIILA VEFITIAFAE QLRSMEKDPE KKKYPGGAFD PLGFSKDPAK LQEFKVKEIK NGRLALLAFV G FCVQQSAY PGTGPLENLA THLADPWHNN IGDVVIPRSI FP

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Macromolecule #2: Photosystem I chlorophyll a/b-binding protein 2 (Lhca2)

MacromoleculeName: Photosystem I chlorophyll a/b-binding protein 2 (Lhca2)
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Posidonia oceanica (plant)
Molecular weightTheoretical: 23.094199 KDa
SequenceString: AAASERPLWF PGSNPPEWLD GSLPGDFGFD PLGLSSDPES LKWNVQAEIV HCRWAMLGAA GIFVPELLTK LGILNTPSWY TAGELEYFT DTTTLFIIEL VLIGWAEGRR WADMINPGCV NTDPVFPNNK LTGTDVGYPG GLWFDPLGWG SGSPEKIKEL R TKEIKNGR ...String:
AAASERPLWF PGSNPPEWLD GSLPGDFGFD PLGLSSDPES LKWNVQAEIV HCRWAMLGAA GIFVPELLTK LGILNTPSWY TAGELEYFT DTTTLFIIEL VLIGWAEGRR WADMINPGCV NTDPVFPNNK LTGTDVGYPG GLWFDPLGWG SGSPEKIKEL R TKEIKNGR LAMLAVMGAW FQHIYTGTGP IDNLFAHLAD PGHATIFAAF SPK

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Macromolecule #3: Photosystem I chlorophyll a/b-binding protein 3-1 (Lhca3)

MacromoleculeName: Photosystem I chlorophyll a/b-binding protein 3-1 (Lhca3)
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Posidonia oceanica (plant)
Molecular weightTheoretical: 25.149672 KDa
SequenceString: TSTPPAKQGA GRQLWFASKQ SLSYLDGSLP GDFGFDPLGL SDPEGTGGFI NPRWLAYAEI MNGRFAMLGA AGSIAPELFG KLGLIPQET ALPWFQSGVI PPAGTYSYWA DPYTLFVFEL ALMGFAEHRR YQDWSKPGSM GKQYFLGLEK GLGGSGDPAY P GGPFFNPL ...String:
TSTPPAKQGA GRQLWFASKQ SLSYLDGSLP GDFGFDPLGL SDPEGTGGFI NPRWLAYAEI MNGRFAMLGA AGSIAPELFG KLGLIPQET ALPWFQSGVI PPAGTYSYWA DPYTLFVFEL ALMGFAEHRR YQDWSKPGSM GKQYFLGLEK GLGGSGDPAY P GGPFFNPL GFGKDEKSMK ELKLKEIKNG RLAMLAILGY FIQGLVTGAS PLQNLLDHLA DPVNNNVLTS LKFH

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Macromolecule #4: Chlorophyll a-b binding protein 4 (Lhca4)

MacromoleculeName: Chlorophyll a-b binding protein 4 (Lhca4) / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Posidonia oceanica (plant)
Molecular weightTheoretical: 22.15815 KDa
SequenceString: KKGEWLPGLA SPNYLNGSLP GDNGFDPLGL GEDPESLKWF VQAELQNGRW AMLAVAGVLL PEVLTKIGII NVPEWYDAGK SEYFASSST LFVIEFILFH YVEIRRWQDI KNPGCVNQDP IFKNYSLPPG EVGYPGGIFN PLNFAPSLEA KEKEIANGRL A MLAFLGFL ...String:
KKGEWLPGLA SPNYLNGSLP GDNGFDPLGL GEDPESLKWF VQAELQNGRW AMLAVAGVLL PEVLTKIGII NVPEWYDAGK SEYFASSST LFVIEFILFH YVEIRRWQDI KNPGCVNQDP IFKNYSLPPG EVGYPGGIFN PLNFAPSLEA KEKEIANGRL A MLAFLGFL VQHNVTGKGP IDNLLQHISD PWHNTIIQTF SG

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Macromolecule #5: Photosystem I P700 chlorophyll a apoprotein A1 (PsaA)

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Posidonia oceanica (plant)
Molecular weightTheoretical: 83.217234 KDa
SequenceString: MIIRSPEPEV KIVVDRDPVK TSFEEWARPG HFSRTIAKGP DTTTWIWNLH ADAHDFDSHT SDLEEISRKV FSAHFGQLSI IFLWLSGMY FHGARFSNYE AWLSDPTHIG PSAQVVWPIV GQEILNGDVG GGFRGIQITS GFFQLWRASG ITSELQLYCT A IGALVFAS ...String:
MIIRSPEPEV KIVVDRDPVK TSFEEWARPG HFSRTIAKGP DTTTWIWNLH ADAHDFDSHT SDLEEISRKV FSAHFGQLSI IFLWLSGMY FHGARFSNYE AWLSDPTHIG PSAQVVWPIV GQEILNGDVG GGFRGIQITS GFFQLWRASG ITSELQLYCT A IGALVFAS LMLFAGWFHY HKAAPKLAWF QDVESMLNHH LAGLLGLGSL SWAGHQIHIS LPINQFLDAG VDPKEIPLPH EF ILNRDLL AQLYPSFAEG ATPFFTLNWS KYADFLTFRG GLDPITGGLW LSDIAHHHLA IAILFLIAGH MYRTNWGIGH GLK DILEAH KGPFTGQGHK GLYEILTTSW HAQLSLNLAM LGSLTIVVAH HMYSMPPYPY LAIDYGTQLS LFTHHMWIGG FLIV GAAAH AAIFMVRDYD PTTRYNDLLD RVLRHRDAII SHLNWACIFL GFHSFGLYIH NDTMSALGRP QDMFSDTAIQ LQPIF AQWV QNTHALAPGT TAPGATASTS LTWGGGELVA VGGKVALLPI PLGTADFLVH HIHAFTIHVT VLILLKGVLF ARSSRL IPD KANLGFRFPC DGPGRGGTCQ VSAWDHVFLG LFWMYNAISV VIFHFSWKMQ SDVWGTISDQ GVVTHITGGN FAQSSIT IN GWLRDFLWAQ ASQVIQSYGS SLSAYGLFFL GAHFVWAFSL MFLFSGRGYW QELIESIVWA HNKLKVAPAT QPRALSIV Q GRAVGVTHYL LGGIATTWAF FLARIIAVG

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Macromolecule #6: Photosystem I P700 chlorophyll a apoprotein A2 (PsaB)

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Posidonia oceanica (plant)
Molecular weightTheoretical: 82.521711 KDa
SequenceString: MALRFPRFSQ GLAQDPTTRR IWFGIATAHD FESHDDITEE RLYQNIFASH FGQLAIIFLW TSGNLFHVAW QGNFESWVQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA LGPVNIAYSG VYQWWYTIGL RTNEDLYTGA LFLLFLSAIS LIAGWLHLQP K WKPSVSWF ...String:
MALRFPRFSQ GLAQDPTTRR IWFGIATAHD FESHDDITEE RLYQNIFASH FGQLAIIFLW TSGNLFHVAW QGNFESWVQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA LGPVNIAYSG VYQWWYTIGL RTNEDLYTGA LFLLFLSAIS LIAGWLHLQP K WKPSVSWF KNAESRLNHH LSGLFGVSSL AWTGHLVHVA IPASRGEYVR WNNFLDVLPY PQGLGPLFTG QWNLYAQNPD SG SHLFGTS QGAGTAILTL LGGFHPQTQS LWLTDIAHHH LAIAFIFLVA GHMYRTNFGI GHSIKDLLEA HIPPGGRLGR GHK GLYDTI NNSIHFQLGL ALASLGVVTS LVAQHMYSLP AYAFIAQDFT TQAALYTHHQ YIAGFIMTGA FAHGAIFFIR DYNP EQNED NVLARMLDHK EAIISHLSWA SLFLGFHTLG LYVHNDVMLA FGTPEKQILI EPIFAQWIQS AHGKTSYGFD VLLSS TNGP AFNAGRNIWL PGWLNAVNEN SNSLFLTIGP GDFLVHHAIA LGLHTTTLIL VKGALDARGS KLMPDKKDFG YSFPCD GPG RGGTCDISAW DAFYLAVFWM LNTIGWVTFY WHWKHITLWQ GNVSQFNESS TYLMGWLRDY LWLNSSQLIN GYNPFGM NS LSVWAWMFLF GHLVWATGFM FLISWRGYWQ ELIETLAWAH ERTPLANLIR WRDKPVALSI VQARLVGLAH FSVGYIFT Y AAFLIASTSG KFG

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Macromolecule #7: Photosystem I iron-sulfur center (PsaC)

MacromoleculeName: Photosystem I iron-sulfur center (PsaC) / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Posidonia oceanica (plant)
Molecular weightTheoretical: 9.040499 KDa
SequenceString:
MSHSVKIYDT CIGCTQCVRA CPTDVLEMIP WDGCKAKQIA SAPRTEDCVG CKRCESACPT DFLSVRVYLY HETTRSMALA Y

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Macromolecule #8: Photosystem I reaction center subunit II-1 (PsaD)

MacromoleculeName: Photosystem I reaction center subunit II-1 (PsaD) / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Posidonia oceanica (plant)
Molecular weightTheoretical: 17.169596 KDa
SequenceString:
SATQEATTEA PVGFTPPELD PNTPSPIFGG STGGLLRKAQ VEEFYVITWT SPKEQVFEMP TGGAAIMREG PNLLKLARKE QCLALGTRL RSKYKIDYQF YRVFPNGEVQ YLHPKDGIYP EKVNAGRLGV GLNMRSIGKN VSPIEVKFTG KQPYDL

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Macromolecule #9: Photosystem I reaction center subunit IV A (PsaE1)

MacromoleculeName: Photosystem I reaction center subunit IV A (PsaE1) / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Posidonia oceanica (plant)
Molecular weightTheoretical: 10.392691 KDa
SequenceString:
ASGEETAPVA EEKRPAADPP AAAKPKPEKI GPKRGTKVKI LRRESYWFNG VGSVVTVDQD PNSRYPVVVR FNKVNYNNVF TNNYAFDEI LEVK

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Macromolecule #10: Photosystem I reaction center subunit III (PsaF)

MacromoleculeName: Photosystem I reaction center subunit III (PsaF) / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Posidonia oceanica (plant)
Molecular weightTheoretical: 17.75967 KDa
SequenceString:
DIAGLTPCKE SKAFAKREKQ SLKKLESSLK KYAPDSAPAL AIKASMEKTK RRFDNYGKQG LLCGSDGLPH LIVSGDQRHW GEFITPGIL FLYIAGWIGW VGRSYLIAIR DEKKPTMKEI IIDVPLASKL IWRGFIWPVA AYRELINGDL VVDDADVSVT

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Macromolecule #11: Photosystem I reaction center subunit V (PsaG)

MacromoleculeName: Photosystem I reaction center subunit V (PsaG) / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Posidonia oceanica (plant)
Molecular weightTheoretical: 11.023403 KDa
SequenceString:
ELNPQVVICL STGLSLFLGR FVFFNFQREN VAKQGLPKQN GISHFEAGDE RAKEYVGLLK SNDPVGFNIV DVLAWGSIGH IVAYYVLAT SSNGYDPNFF G

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Macromolecule #12: Photosystem I reaction center subunit VI-1 (PsaH1)

MacromoleculeName: Photosystem I reaction center subunit VI-1 (PsaH1) / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Posidonia oceanica (plant)
Molecular weightTheoretical: 10.508876 KDa
SequenceString:
KYGDKSVYFD LEDLPNTTGQ WDLYGSDAPS PYNSLQSKFF ETFAAPFTKR GLLLKFLILG GGFTLAYYSS TASGDILPIK KGPQLPPEL GPRDKK

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Macromolecule #13: Photosystem I reaction center subunit VIII (PsaI)

MacromoleculeName: Photosystem I reaction center subunit VIII (PsaI) / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Posidonia oceanica (plant)
Molecular weightTheoretical: 3.94082 KDa
SequenceString:
MTDLNLPSIF VPLVGLVFPA IAMASLFLHV QKNKIV

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Macromolecule #14: Photosystem I reaction center subunit IX (PsaJ)

MacromoleculeName: Photosystem I reaction center subunit IX (PsaJ) / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Posidonia oceanica (plant)
Molecular weightTheoretical: 4.777646 KDa
SequenceString:
MRDIKTYLSV APVLTTLWFG SLAGLLIEIN RLFPDALSFP FF

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Macromolecule #15: Photosystem I reaction center subunit psaK (PsaK)

MacromoleculeName: Photosystem I reaction center subunit psaK (PsaK) / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Posidonia oceanica (plant)
Molecular weightTheoretical: 8.471875 KDa
SequenceString:
DFIGSSTNII MVTTTSLMLF AGRFGLAPSA NRKATAGLKL EVRDSGLQTG DPAGFTLADT LACGVVGHIM GVGIVLGLKS IGAI

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Macromolecule #16: Photosystem I reaction center subunit XI (PsaL)

MacromoleculeName: Photosystem I reaction center subunit XI (PsaL) / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Posidonia oceanica (plant)
Molecular weightTheoretical: 18.128881 KDa
SequenceString:
AIQAEKPTTF QVIEPINGDP FIGSLETPVT SSPLVAWYLS NLPAYRTAVS PLLRGIEVGL AHGYLLVGPF VITGPLRNTP YHGAAGSLA AGGLVVILSI CLTMYGISSF KEGEPSCAPG LTLTGRKKEA DKLQTADGWA QFTGGFFFGG ISGVIWAYFL L YVLDLPYY IK

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Macromolecule #17: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 17 / Number of copies: 12 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Macromolecule #18: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 18 / Number of copies: 143 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #19: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

MacromoleculeName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 19 / Number of copies: 5 / Formula: LUT
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-LUT:
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Macromolecule #20: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

MacromoleculeName: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 20 / Number of copies: 4 / Formula: XAT
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-XAT:
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Macromolecule #21: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 21 / Number of copies: 28 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #22: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 22 / Number of copies: 6 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

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Macromolecule #23: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 23 / Number of copies: 7 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Macromolecule #24: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 24 / Number of copies: 4 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #25: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 25 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #26: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 26 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #27: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 27 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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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
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHepes
0.01 %C24H46O11n-DODECYL-beta-D-MALTOSIDE
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 120603
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

5zji


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF ChimeraX (ver. 1.9)
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9s1l:
Cryo-EM structure of Posidonia oceanica PSI-LHCI supercomplex

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