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- EMDB-60032: PSI-FCPI-L in Thalassiosira pseudonana -

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Basic information

Entry
Database: EMDB / ID: EMD-60032
TitlePSI-FCPI-L in Thalassiosira pseudonana
Map data
Sample
  • Complex: Tp-PSI-FCPI-L
    • Protein or peptide: x 25 types
  • Ligand: x 12 types
Keywordsphotosystem I / PHOTOSYNTHESIS
Function / homology
Function and homology information


light-harvesting complex / photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane ...light-harvesting complex / photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / membrane
Similarity search - Function
Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA / 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
Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit II / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Fucoxanthin chl a/c light-harvesting protein, major type ...Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit II / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Fucoxanthin chl a/c light-harvesting protein, major type / Uncharacterized protein / Fucoxanthin chlorophyll a/c light-harvesting protein / Uncharacterized protein / Fucoxanthin chl a/c light-harvesting protein / Fucoxanthin chl a/c light-harvesting protein / Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type / Fucoxanthin chl a/c light-harvesting protein / Fucoxanthin chlorophyll a/c light-harvesting protein / Uncharacterized protein / Fucoxanthin chl a/c light-harvesting protein, lhcr type / Pt17531-like protein / PSAE, photosystem I reaction center subunit
Similarity search - Component
Biological speciesThalassiosira pseudonana CCMP1335 (Diatom)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsFeng Y / Li Z / Wang W / Shen JR
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences2020081 China
CitationJournal: J Integr Plant Biol / Year: 2025
Title: Structures of PSI-FCPI from Thalassiosira pseudonana grown under high light provide evidence for convergent evolution and light-adaptive strategies in diatom FCPIs.
Authors: Yue Feng / Zhenhua Li / Yang Yang / Lili Shen / Xiaoyi Li / Xueyang Liu / Xiaofei Zhang / Jinyang Zhang / Fei Ren / Yuan Wang / Cheng Liu / Guangye Han / Xuchu Wang / Tingyun Kuang / Jian- ...Authors: Yue Feng / Zhenhua Li / Yang Yang / Lili Shen / Xiaoyi Li / Xueyang Liu / Xiaofei Zhang / Jinyang Zhang / Fei Ren / Yuan Wang / Cheng Liu / Guangye Han / Xuchu Wang / Tingyun Kuang / Jian-Ren Shen / Wenda Wang /
Abstract: Diatoms rely on fucoxanthin chlorophyll a/c-binding proteins (FCPs) for light harvesting and energy quenching under marine environments. Here we report two cryo-electron microscopic structures of ...Diatoms rely on fucoxanthin chlorophyll a/c-binding proteins (FCPs) for light harvesting and energy quenching under marine environments. Here we report two cryo-electron microscopic structures of photosystem I (PSI) with either 13 or five fucoxanthin chlorophyll a/c-binding protein Is (FCPIs) at 2.78 and 3.20 Å resolutions from Thalassiosira pseudonana grown under high light (HL) conditions. Among them, five FCPIs are stably associated with the PSI core, these include Lhcr3, RedCAP, Lhcq8, Lhcf10, and FCP3. The eight additional Lhcr-type FCPIs are loosely associated with the PSI core and detached under the present purification conditions. The pigments of this centric diatom showed a higher proportion of chlorophylls a, diadinoxanthins, and diatoxanthins; some of the chlorophyll as and diadinoxanthins occupy the locations of fucoxanthins found in the huge PSI-FCPI from another centric diatom Chaetoceros gracilis grown under low-light conditions. These additional chlorophyll as may form more energy transfer pathways and additional diadinoxanthins may form more energy dissipation sites relying on the diadinoxanthin-diatoxanthin cycle. These results reveal the assembly mechanism of FCPIs and corresponding light-adaptive strategies of T. pseudonana PSI-FCPI, as well as the convergent evolution of the diatom PSI-FCPI structures.
History
DepositionMay 6, 2024-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60032.png

Downloads & links

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Map

FileDownload / File: emd_60032.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 512 pix.
= 563.2 Å		1.1 Å/pix.
x 512 pix.
= 563.2 Å		1.1 Å/pix.
x 512 pix.
= 563.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.088
Minimum - Maximum-0.47193396 - 1.7185627
Average (Standard dev.)-0.00010491457 (±0.025269913)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 563.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60032_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_60032_half_map_2.map
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Sample components

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Entire : Tp-PSI-FCPI-L

EntireName: Tp-PSI-FCPI-L
Components
  • Complex: Tp-PSI-FCPI-L
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcq8
    • Protein or peptide: Fucoxanthin chl a/c light-harvesting protein, major type
    • Protein or peptide: Pt17531-like protein
    • Protein or peptide: Tp-RedCAP
    • Protein or peptide: Fucoxanthin chl a/c light-harvesting protein
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: Photosystem I reaction center subunit II
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I reaction center subunit III
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: Tp-PsaR
    • Protein or peptide: Tp-Lhcr20
    • Protein or peptide: Fucoxanthin chl a/c light-harvesting protein, lhcr type
    • Protein or peptide: Fucoxanthin chl a/c light-harvesting protein
    • Protein or peptide: Fucoxanthin chl a/c light-harvesting protein
    • Protein or peptide: Fucoxanthin chlorophyll a/c light-harvesting protein
    • Protein or peptide: Fucoxanthin chlorophyll a/c light-harvesting protein
    • Protein or peptide: Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type
    • Protein or peptide: Tp-Lhcr18
    • Protein or peptide: Photosystem I reaction center subunit Psa29
  • Ligand: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
  • Ligand: CHLOROPHYLL A
  • Ligand: Chlorophyll c1
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: PHYLLOQUINONE
  • Ligand: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Supramolecule #1: Tp-PSI-FCPI-L

SupramoleculeName: Tp-PSI-FCPI-L / type: complex / ID: 1 / Parent: 0
Macromolecule list: #2-#3, #23, #4, #7, #13, #24-#25, #14-#16, #18-#22, #5-#6, #8-#12, #1, #17
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)

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Macromolecule #1: Tp-Lhcr18

MacromoleculeName: Tp-Lhcr18 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 16.623979 KDa
SequenceString:
YNHNSGGVNF KGDTFQFDPL GLSETYAPLV PFFRESEIRH GRTAMLAVTG FIVQDFVRIP GDAYSFEAVP KTVGAHDALL EGPMHQLLL WISLWDIVIT YPSIQATMKG EREPGDFGWK WLAPKDEATL KKYEMNELLN GRLAMMAVG

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Macromolecule #2: Fucoxanthin chlorophyll a/c-binding protein Lhcq8

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcq8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 18.249709 KDa
SequenceString:
YASELDSMTG TGIESPKVFD PLNLSDYVPV DWARRAELSN GRSAMLATVG WFFPKVFGTF DSTDVTTTDP IDAIMQADPQ WWAQWILIC GVFETWKYKK EMEGKSFLGG ADPAVDYLKL WPADAAAQEE MKTKELKNAR LAMIGIAGFA ANHFIPGSCP V PDFIA

UniProtKB: Uncharacterized protein

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Macromolecule #3: Fucoxanthin chl a/c light-harvesting protein, major type

MacromoleculeName: Fucoxanthin chl a/c light-harvesting protein, major type
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 18.537982 KDa
SequenceString:
ADFSGEIGAA NAELGCWDPL NFCTDQASFD KMRYAELKHG RVAQLAAWGY ATTWSGARFP GCEDFPAGHE AVLKIGTENL IPVLVVAGA LETLWKQKEG SFPGDFSATS FPVGFGPFAK TEADMIDLRT KELNNGRAAM MGILGMIVHE QIDGKPFIFF D KFEIYAPF GN

UniProtKB: Fucoxanthin chl a/c light-harvesting protein, major type

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Macromolecule #4: Tp-RedCAP

MacromoleculeName: Tp-RedCAP / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 20.184035 KDa
SequenceString:
SVFDDAVKDW AEEYPQFAAW GWGPSVQAEI WNGRHAMFGW VVMCACAYAK GHGLIPDADQ TLDLKEWGTL ATISGKNTIT NERAIILIA NVHALMVGLA ATISPNSFAD TLLLDPNHPM YEWQMERNSK LGGVMPNLGK MGVTPEAELA NGRMAMMGII T CIAYSGIQ GQSMIDTINE WVGGAYF

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Macromolecule #5: Tp-Lhcr20

MacromoleculeName: Tp-Lhcr20 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 18.561406 KDa
SequenceString:
FANGLVGGEG PEPMPFNLVG EKNAKNFDPA GFSERAPEWI NWFREAELKH GRQAMLAVVG MVVPEFVRIP GEAFSFEAIP NVLDAHDAL LDTSMKQILL WISLMEAMSL GALSNMNEFD REPGNFGFDP LGMMPKDAAK AKEMQLKELK NGRLAMVAIG G MVHGAITT GH

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Macromolecule #6: Fucoxanthin chl a/c light-harvesting protein, lhcr type

MacromoleculeName: Fucoxanthin chl a/c light-harvesting protein, lhcr type
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 18.926678 KDa
SequenceString:
AEMSKAMPFL INPANTDGLI GSNGFDPLGF SDTFDIKWLQ ESEIKHGRVA MLASAGFIAS QFVNFPMYSS MHVDDSNMAP TVVGISAML QIVCAAGVEE WRTYKGQVTM EDMFTGDMAD RTPGDFGFDP MGQLKGKSEA AVNEMKLKEI KNGRLAMLAI G GMIHHNFV TGEALF

UniProtKB: Fucoxanthin chl a/c light-harvesting protein, lhcr type

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Macromolecule #7: Fucoxanthin chl a/c light-harvesting protein

MacromoleculeName: Fucoxanthin chl a/c light-harvesting protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 18.522117 KDa
SequenceString:
EMSKSIPFLT VPEKLDGSMA GDVGFDPMGL SDIQTDLNYA RWAELKHGRI CMLAVVGMVW QEYGPHLPGD AYATKDPWEA ISSVGFASN FQTLLAIGVV ELANWNKYYG DGTPGDIGWT GGQLSKMNDA QIKTRMESEI VHCRLAMIAF IGATHQTFLL H KGLLDFSY

UniProtKB: Fucoxanthin chl a/c light-harvesting protein

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Macromolecule #8: Fucoxanthin chl a/c light-harvesting protein

MacromoleculeName: Fucoxanthin chl a/c light-harvesting protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 18.70643 KDa
SequenceString:
AEKSASLPFL EAPPNLDGGV GDLGFDPFRF SDFVPIDFLR EAELKHGRIC MMAWLGFVAV DMGFRVYPAA EGFESLTSIT AHDAAVEQG GMSQMLLWFS LLEVFDTIAV QQMLEGSGRA PGDFGLDGGF LKGKSQAEID TMKLKEIVHC RLAMFAFSGV V TQAVLTQG PFPY

UniProtKB: Fucoxanthin chl a/c light-harvesting protein

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Macromolecule #9: Fucoxanthin chl a/c light-harvesting protein

MacromoleculeName: Fucoxanthin chl a/c light-harvesting protein / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 19.792484 KDa
SequenceString:
AERSPSLPFM NKPALLDPSM PGYKGFDPLG LSNIDDVGID LYWLREAEIK HARVAMLAVA GAVWVEAFGP APGCEAATAK NQMDAFWQI WNSHPQYIAA SLVFIMIAEA VSGISTTTGR ESGEREPGFF GFGSNFPKTD ADMKKMQDKE LENGRLAMWA A MGLIFQGS ANHMGGLEAL GATFN

UniProtKB: Fucoxanthin chl a/c light-harvesting protein

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Macromolecule #10: Fucoxanthin chlorophyll a/c light-harvesting protein

MacromoleculeName: Fucoxanthin chlorophyll a/c light-harvesting protein / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 19.044955 KDa
SequenceString:
AFNPEMAGEV FDPMGFGKMH EIKGAFPNMF PNPQFLEESE IKHGRMAMLA WTGVWATESG LHFPGAPVAD DWTTALGVWA REDPGGFGI VLLLLSIAEG EGVSHAGDNF RGVSKKTPGD MGFDWMGMTK KLSADKLERY QTVEKKNGRA AMIAMASLFA M KAIPGSVP IMDMLGAN

UniProtKB: Fucoxanthin chlorophyll a/c light-harvesting protein

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Macromolecule #11: Fucoxanthin chlorophyll a/c light-harvesting protein

MacromoleculeName: Fucoxanthin chlorophyll a/c light-harvesting protein / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 23.791238 KDa
SequenceString: AMPDRMWNKM VDKTQRSKAM PFLPRPINLD GSYVGDVGFD PFYLSSIDKN FAGFIQPPSW EETNGLPTLY WMREAELKHG RIAMMAFAG WLATDFGVRF PGAGEPYTSV PNAFSAHNIM VDSGAMWVML SLIGFIEIST AAVLVEVSKG ENDREAGDFC F DPLGFCKG ...String:
AMPDRMWNKM VDKTQRSKAM PFLPRPINLD GSYVGDVGFD PFYLSSIDKN FAGFIQPPSW EETNGLPTLY WMREAELKHG RIAMMAFAG WLATDFGVRF PGAGEPYTSV PNAFSAHNIM VDSGAMWVML SLIGFIEIST AAVLVEVSKG ENDREAGDFC F DPLGFCKG KSADAINTMK LKELQNGRAA MMAFGGLATQ TALGGVDFPY LVPYPNVAD

UniProtKB: Fucoxanthin chlorophyll a/c light-harvesting protein

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Macromolecule #12: Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type

MacromoleculeName: Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 18.608336 KDa
SequenceString:
AKSKALPWLP NPSNLDGRIG ANGFDPLGIS EYFPVDYLVE SEIKHGRVCM MAWAGYVAVD LGARIYPLPE SMQGVTSATA HDPAVAFGS MGNMFIWIAL FEMVGWIGLS QTLQGSGREP GDFGWGKQFM GKTQAEIDTM KLKELTNGRA AMLAFAGVVT Q SVLYDKGF PYF

UniProtKB: Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type

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Macromolecule #13: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 82.691633 KDa
SequenceString: SKNVQVFVEK DAVETSFAKW AQPGHFSRTL AKGPKTTTWI WNLHADAHDF DSQTSSLEEV SRKIFSAHFG QLAIIFLWIS GMHFHGAYF SNYSAWLTDP ISIKQSSQVV WPIVGQEILN ADVGGNFQGI QTTSGWFQMW RAEGITSEVE LYWTAIGGLA M SAIMLFAG ...String:
SKNVQVFVEK DAVETSFAKW AQPGHFSRTL AKGPKTTTWI WNLHADAHDF DSQTSSLEEV SRKIFSAHFG QLAIIFLWIS GMHFHGAYF SNYSAWLTDP ISIKQSSQVV WPIVGQEILN ADVGGNFQGI QTTSGWFQMW RAEGITSEVE LYWTAIGGLA M SAIMLFAG WFHYHKAAPK LEWFQNAESM MNHHLAGLLG LGCLSWSGHQ IHIALPINKL LDAGVSPQEI PLPHEFLINR DL MAQLYPS FSKGLAPFFG GNWGEYSDFL TFKGGLNPVT GGLWLSDIAH HHLALSVLFI IAGHMYRTNW GIGHNMKEIL EAH KGPFTG EGHKGLYEIL TTSWHAQLAI NLAMMGSLSI IVAHHMYAMP PYPYLATDYA TQLSLFTHHM WIGGFCVVGG AAHG AIFMV RDYTPANNYN NLLDRVLRHR DAIISHLNWV CIFLGCHAFG FYIHNDTMRA LGRPQDMFSD KAIQLQPIFA QWIQN IHLL APGTTAPNAL ATTSYAFGGD VIEVGGKIAM MPIKLGTADF MVHHIHAFTI HVTVLILLKG VLYARSSKLI PDKANL GFR FPCDGPGRGG TCQSSSWDHV FLGLFWMYNS ISVVIFHFSW KMQSDVWGTI TPDGAISHIT GGNFAQSSIT INGWLRD FL WSQASQVIQS YGSASSAYGL IFLGAHFIWA FSLMFLFSGR GYWQELIESI VWAHNKLNFA PTIQPRALSI TQGRAVGL A HYLLGGIGTT WAFFLARAIS IT

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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Macromolecule #14: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 14.732663 KDa
SequenceString:
PFPTFGGSTG GWLRAAEVEE KYAITWTSTK EQIFEMPTGG AAIMRNGENL LYLARKEQCL ALSTQLRTFK INDYKIYRIF PSGEVQYLH PKDGVFPEKV NPGRTSVNSR GFSIGKNPNP ASIKFSGITT YES

UniProtKB: Photosystem I reaction center subunit II

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Macromolecule #15: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 7.133023 KDa
SequenceString:
MIDRNSKVRI LRKESYWFNQ IGTVATVDQS GIRYPAVVRF ESVNYAGTNT NNFALDELVE VK

UniProtKB: PSAE, photosystem I reaction center subunit

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Macromolecule #16: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 17.617021 KDa
SequenceString:
EIGGLTKCSE SAAFTKRLNA SVKKLEQRAS QYEADSPPAL ALKQQVERTQ ARFDKYSRSE LLCGADGLPH LVADGRWSHA AEFILPGFG FIYISGWIGW VGRKYLRAVS TSANPSESEI IINVPLALKI MTTGYIWPIS AWQELISNDL VAVSEEITVS P

UniProtKB: Photosystem I reaction center subunit III

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Macromolecule #17: Photosystem I reaction center subunit Psa29

MacromoleculeName: Photosystem I reaction center subunit Psa29 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 13.9363 KDa
SequenceString:
VDLDYGMKNS YVPATGGDGG QGQFGAQSPN DWRVAGTSPV GETSYAGAAD GGEEPWFAEA ISTVSLDLQK ADETLKAFTK DAAAFKIEE FAAEKPYGFT SSDAAMEELV GKLGYSKFLE MSTKQLMKTW GT

UniProtKB: Uncharacterized protein

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Macromolecule #18: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 3.604257 KDa
SequenceString:
AASFLPSILV PLVGLIFPAF SMALFFLYVQ TDD

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #19: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 4.707531 KDa
SequenceString:
MNDFQKYLST APVLLTLWMT FTAGFIIEVN RFFPDMLGLY

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #20: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 15.469909 KDa
SequenceString:
ANFIKPYNDD PFVGHLATPI TSSSLTRALL KNLPAYRFGL TPLLRGLEIG LAHGYFLIGP FAQLGPLRNS DIGLLAGFLS TIGLILILT LGLTIYGAAA FGQEKSNGSE LQTKKSWDQF KGGFFVGACG SAGFAFICLS SIPTFAL

UniProtKB: Photosystem I reaction center subunit XI

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Macromolecule #21: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 3.143825 KDa
SequenceString:
MITDFQVYIA LMAALLASVL AIRLGATLY

UniProtKB: Photosystem I reaction center subunit XII

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Macromolecule #22: Tp-PsaR

MacromoleculeName: Tp-PsaR / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 9.740316 KDa
SequenceString:
DMTWEGEYPP SKVLGPIMSK MPSGLLAIIS MASLGVCVYS CVQTGFLLRE PGAIENGSWV RWYYVVEGLG GPLAWGTHVA SWIQRKNGM

UniProtKB: Uncharacterized protein

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Macromolecule #23: Pt17531-like protein

MacromoleculeName: Pt17531-like protein / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 18.091611 KDa
SequenceString:
AWRDEVVVGI TAPVGFFDPL GLSKGKDDAT MAYYREAELK NGRVAMAACL GWYLNAGGVH PAFNSELSND PLKAMVELPA VGWLQFVLG CGAIEWLGQQ IKERPGYVPG DLLGASYWVD NSDEGWVMYQ NKELNNGRLA MLAIVGMVYQ DVFVGDYGDM M YKQL

UniProtKB: Pt17531-like protein

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Macromolecule #24: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 82.04268 KDa
SequenceString: ATKFPKFSQA LAQDPATRRI WYGIATAHDL EAHDGMTEEN LYQKIFASHF GHLAIIFLWT SGNLFHVAWQ GNFEKWVSNP LKTRPIAHS IWDPHFGESA LKAFSKGNTY PVNITFSGLY QWWYTIGFRT NQELYKGSIG LLLLASVLLI AGWLHLQPKF R PSLSWFKN ...String:
ATKFPKFSQA LAQDPATRRI WYGIATAHDL EAHDGMTEEN LYQKIFASHF GHLAIIFLWT SGNLFHVAWQ GNFEKWVSNP LKTRPIAHS IWDPHFGESA LKAFSKGNTY PVNITFSGLY QWWYTIGFRT NQELYKGSIG LLLLASVLLI AGWLHLQPKF R PSLSWFKN NESRLNHHLS GLLGFSSLAW TGHLVHVAIP ASRGVHVGWD NFLTTPPHPA GLTPFFTGNW TVYAENPDSA TH VFNTSEG SGTAILTFLG GFHPQTQSLW LSDMAHHHLA IAVVFIVAGH MYRTNFGIGH NMKEILDAHR PPGGRLGAGH VGL FETITN SLHMQLGLAL ACLGVATSLT AQHMYALTPY AYLSKDFTTE AALYTHHQYI AGFLMVGAFA HGAIFFVRDY DPEL NKNNV LARMLEHKEA IISHLSWASL FLGFHTLGLY IHNDTVVAFG QPEKQILFEP LFAEYIQAAS GKAVYQFNVL LASST SPAT AAGNQVWLPG WLEAINNPKT DLFLKIGPGD FLVHHAIALG LHVTALILVK GALDARGSKL MPDKKDFGYS FPCDGP GRG GTCDISAWDA FYLAMFWMLN TIGWVTFYWH WKHMTIWGGN PGQFDESSNY IMGWLRDYLW LNSSPLINGY NPFGMNN LS VWSWMFLFGH LIWATGFMFL ISWRGYWQEL IETLVWAHER TPLANLIRWR DKPVALSIVQ ARLVGLVHFS VGYILTYA A FVIASTSGKF A

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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Macromolecule #25: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 8.675973 KDa
SequenceString:
SHTVKIYDTC IGCTQCVRAC PTDVLEMVPW DGCKSGQIAS SPRVEDCVGC KRCETACPTD FLSVRVYLGA ETTRSLGLAY

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #26: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,be...

MacromoleculeName: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
type: ligand / ID: 26 / Number of copies: 27 / Formula: DD6
Molecular weightTheoretical: 582.855 Da
Chemical component information

ChemComp-DD6:
(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol

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Macromolecule #27: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 27 / Number of copies: 229 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #28: Chlorophyll c1

MacromoleculeName: Chlorophyll c1 / type: ligand / ID: 28 / Number of copies: 15 / Formula: KC1
Molecular weightTheoretical: 610.941 Da
Chemical component information

ChemComp-KC1:
Chlorophyll c1

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Macromolecule #29: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 29 / Number of copies: 13 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #30: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5...

MacromoleculeName: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate
type: ligand / ID: 30 / Number of copies: 38 / Formula: A86
Molecular weightTheoretical: 658.906 Da

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Macromolecule #31: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 31 / Number of copies: 15 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #32: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 32 / Number of copies: 21 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #33: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

MacromoleculeName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
type: ligand / ID: 33 / Number of copies: 1 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

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Macromolecule #34: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 34 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #35: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},...

MacromoleculeName: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen- ...Name: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol
type: ligand / ID: 35 / Number of copies: 1 / Formula: ET4
Molecular weightTheoretical: 566.856 Da
Chemical component information

ChemComp-ET4:
(1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol

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Macromolecule #36: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 36 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #37: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 37 / 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: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129097
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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