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- EMDB-38457: PSI-FCPI of the diatom Thalassiosira pseudonana CCMP1335 -

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Basic information

Entry
Database: EMDB / ID: EMD-38457
TitlePSI-FCPI of the diatom Thalassiosira pseudonana CCMP1335
Map data
Sample
  • Complex: PSI-FCPI
    • Protein or peptide: x 17 types
  • Ligand: x 15 types
KeywordsPhotosystem I / ELECTRON TRANSPORT / 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 / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus ...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 / 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 IV / 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 ...Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IV / 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 chl a/c light-harvesting protein / Uncharacterized protein / Pt17531-like protein
Similarity search - Component
Biological speciesThalassiosira pseudonana CCMP1335 (Diatom)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsKato K / Nakajima Y / Shen JR / Nagao R
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Elife / Year: 2024
Title: Structural basis for molecular assembly of fucoxanthin chlorophyll /-binding proteins in a diatom photosystem I supercomplex.
Authors: Koji Kato / Yoshiki Nakajima / Jian Xing / Minoru Kumazawa / Haruya Ogawa / Jian-Ren Shen / Kentaro Ifuku / Ryo Nagao /
Abstract: Photosynthetic organisms exhibit remarkable diversity in their light-harvesting complexes (LHCs). LHCs are associated with photosystem I (PSI), forming a PSI-LHCI supercomplex. The number of LHCI ...Photosynthetic organisms exhibit remarkable diversity in their light-harvesting complexes (LHCs). LHCs are associated with photosystem I (PSI), forming a PSI-LHCI supercomplex. The number of LHCI subunits, along with their protein sequences and pigment compositions, has been found to differ greatly among the PSI-LHCI structures. However, the mechanisms by which LHCIs recognize their specific binding sites within the PSI core remain unclear. In this study, we determined the cryo-electron microscopy structure of a PSI supercomplex incorporating fucoxanthin chlorophyll /-binding proteins (FCPs), designated as PSI-FCPI, isolated from the diatom CCMP1335. Structural analysis of PSI-FCPI revealed five FCPI subunits associated with a PSI monomer; these subunits were identified as RedCAP, Lhcr3, Lhcq10, Lhcf10, and Lhcq8. Through structural and sequence analyses, we identified specific protein-protein interactions at the interfaces between FCPI and PSI subunits, as well as among FCPI subunits themselves. Comparative structural analyses of PSI-FCPI supercomplexes, combined with phylogenetic analysis of FCPs from and the diatom , underscore the evolutionary conservation of protein motifs crucial for the selective binding of individual FCPI subunits. These findings provide significant insights into the molecular mechanisms underlying the assembly and selective binding of FCPIs in diatoms.
History
DepositionDec 26, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38457.png

Downloads & links

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Map

FileDownload / File: emd_38457.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 254 pix.
= 191.008 Å		0.75 Å/pix.
x 254 pix.
= 191.008 Å		0.75 Å/pix.
x 254 pix.
= 191.008 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.752 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.040055446 - 0.097367026
Average (Standard dev.)0.0005549062 (±0.004254923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions254254254
Spacing254254254
CellA=B=C: 191.008 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_38457_additional_1.map
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Half map: #2

Fileemd_38457_half_map_1.map
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Half map: #1

Fileemd_38457_half_map_2.map
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Sample components

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Entire : PSI-FCPI

EntireName: PSI-FCPI
Components
  • Complex: PSI-FCPI
    • 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: Photosystem I reaction center subunit Psa29
    • Protein or peptide: Unknown protein
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein RedCAP
    • Protein or peptide: Fucoxanthin chl a/c light-harvesting protein
    • Protein or peptide: Pt17531-like protein
    • Protein or peptide: Fucoxanthin chl a/c light-harvesting protein, major type
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcq8
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: UNKNOWN LIGAND
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: Zeaxanthin
  • Ligand: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: Chlorophyll c1
  • 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: water

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Supramolecule #1: PSI-FCPI

SupramoleculeName: PSI-FCPI / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 550 KDa

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Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 83.725828 KDa
SequenceString: MAISSTERRS KNVQVFVEKD AVETSFAKWA QPGHFSRTLA KGPKTTTWIW NLHADAHDFD SQTSSLEEVS RKIFSAHFGQ LAIIFLWIS GMHFHGAYFS NYSAWLTDPI SIKQSSQVVW PIVGQEILNA DVGGNFQGIQ TTSGWFQMWR AEGITSEVEL Y WTAIGGLA ...String:
MAISSTERRS KNVQVFVEKD AVETSFAKWA QPGHFSRTLA KGPKTTTWIW NLHADAHDFD SQTSSLEEVS RKIFSAHFGQ LAIIFLWIS GMHFHGAYFS NYSAWLTDPI SIKQSSQVVW PIVGQEILNA DVGGNFQGIQ TTSGWFQMWR AEGITSEVEL Y WTAIGGLA MSAIMLFAGW FHYHKAAPKL EWFQNAESMM NHHLAGLLGL GCLSWSGHQI HIALPINKLL DAGVSPQEIP LP HEFLINR DLMAQLYPSF SKGLAPFFGG NWGEYSDFLT FKGGLNPVTG GLWLSDIAHH HLALSVLFII AGHMYRTNWG IGH NMKEIL EAHKGPFTGE GHKGLYEILT TSWHAQLAIN LAMMGSLSII VAHHMYAMPP YPYLATDYAT QLSLFTHHMW IGGF CVVGG AAHGAIFMVR DYTPANNYNN LLDRVLRHRD AIISHLNWVC IFLGCHAFGF YIHNDTMRAL GRPQDMFSDK AIQLQ PIFA QWIQNIHLLA PGTTAPNALA TTSYAFGGDV IEVGGKIAMM PIKLGTADFM VHHIHAFTIH VTVLILLKGV LYARSS KLI PDKANLGFRF PCDGPGRGGT CQSSSWDHVF LGLFWMYNSI SVVIFHFSWK MQSDVWGTIT PDGAISHITG GNFAQSS IT INGWLRDFLW SQASQVIQSY GSASSAYGLI FLGAHFIWAF SLMFLFSGRG YWQELIESIV WAHNKLNFAP TIQPRALS I TQGRAVGLAH YLLGGIGTTW AFFLARAISI T

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 82.173875 KDa
SequenceString: MATKFPKFSQ ALAQDPATRR IWYGIATAHD LEAHDGMTEE NLYQKIFASH FGHLAIIFLW TSGNLFHVAW QGNFEKWVSN PLKTRPIAH SIWDPHFGES ALKAFSKGNT YPVNITFSGL YQWWYTIGFR TNQELYKGSI GLLLLASVLL IAGWLHLQPK F RPSLSWFK ...String:
MATKFPKFSQ ALAQDPATRR IWYGIATAHD LEAHDGMTEE NLYQKIFASH FGHLAIIFLW TSGNLFHVAW QGNFEKWVSN PLKTRPIAH SIWDPHFGES ALKAFSKGNT YPVNITFSGL YQWWYTIGFR TNQELYKGSI GLLLLASVLL IAGWLHLQPK F RPSLSWFK NNESRLNHHL SGLLGFSSLA WTGHLVHVAI PASRGVHVGW DNFLTTPPHP AGLTPFFTGN WTVYAENPDS AT HVFNTSE GSGTAILTFL GGFHPQTQSL WLSDMAHHHL AIAVVFIVAG HMYRTNFGIG HNMKEILDAH RPPGGRLGAG HVG LFETIT NSLHMQLGLA LACLGVATSL TAQHMYALTP YAYLSKDFTT EAALYTHHQY IAGFLMVGAF AHGAIFFVRD YDPE LNKNN VLARMLEHKE AIISHLSWAS LFLGFHTLGL YIHNDTVVAF GQPEKQILFE PLFAEYIQAA SGKAVYQFNV LLASS TSPA TAAGNQVWLP GWLEAINNPK TDLFLKIGPG DFLVHHAIAL GLHVTALILV KGALDARGSK LMPDKKDFGY SFPCDG PGR GGTCDISAWD AFYLAMFWML NTIGWVTFYW HWKHMTIWGG NPGQFDESSN YIMGWLRDYL WLNSSPLING YNPFGMN NL SVWSWMFLFG HLIWATGFMF LISWRGYWQE LIETLVWAHE RTPLANLIRW RDKPVALSIV QARLVGLVHF SVGYILTY A AFVIASTSGK FA

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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Macromolecule #3: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 8.807169 KDa
SequenceString:
MSHTVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCKSGQIA SSPRVEDCVG CKRCETACPT DFLSVRVYLG AETTRSLGLA Y

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #4: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 15.535668 KDa
SequenceString:
MTLNLKTPFP TFGGSTGGWL RAAEVEEKYA ITWTSTKEQI FEMPTGGAAI MRNGENLLYL ARKEQCLALS TQLRTFKIND YKIYRIFPS GEVQYLHPKD GVFPEKVNPG RTSVNSRGFS IGKNPNPASI KFSGITTYES

UniProtKB: Photosystem I reaction center subunit II

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Macromolecule #5: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 7.520497 KDa
SequenceString:
MIDRNSKVRI LRKESYWFNQ IGTVATVDQS GIRYPAVVRF ESVNYAGTNT NNFALDELVE VKKEK

UniProtKB: Photosystem I reaction center subunit IV

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Macromolecule #6: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 20.382461 KDa
SequenceString:
MKRVNLLTLL FAVLIALTPN QALAEIGGLT KCSESAAFTK RLNASVKKLE QRASQYEADS PPALALKQQV ERTQARFDKY SRSELLCGA DGLPHLVADG RWSHAAEFIL PGFGFIYISG WIGWVGRKYL RAVSTSANPS ESEIIINVPL ALKIMTTGYI W PISAWQEL ISNDLVAVSE EITVSPR

UniProtKB: Photosystem I reaction center subunit III

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Macromolecule #7: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 3.919688 KDa
SequenceString:
MAASFLPSIL VPLVGLIFPA FSMALFFLYV QTDDIA

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #8: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 4.854705 KDa
SequenceString:
MNDFQKYLST APVLLTLWMT FTAGFIIEVN RFFPDMLGLY F

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #9: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 15.715207 KDa
SequenceString:
MANFIKPYND DPFVGHLATP ITSSSLTRAL LKNLPAYRFG LTPLLRGLEI GLAHGYFLIG PFAQLGPLRN SDIGLLAGFL STIGLILIL TLGLTIYGAA AFGQEKSNGS ELQTKKSWDQ FKGGFFVGAC GSAGFAFICL SSIPTFALN

UniProtKB: Photosystem I reaction center subunit XI

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Macromolecule #10: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 3.271954 KDa
SequenceString:
MITDFQVYIA LMAALLASVL AIRLGATLYQ

UniProtKB: Photosystem I reaction center subunit XII

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Macromolecule #11: Photosystem I reaction center subunit Psa29

MacromoleculeName: Photosystem I reaction center subunit Psa29 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 20.048312 KDa
SequenceString:
MKIVLIALSA ASVSAFAPNA FGVRRTCYFE WLDLTIPSCG ETTSLNVDLD YGMKNSYVPA TGGDGGQGQF GAQSPNDWRV AGTSPVGET SYAGAADGGE EPWFAEAIST VSLDLQKADE TLKAFTKDAA AFKIEEFAAE KPYGFTSSDA AMEELVGKLG Y SKFLEMST KQLMKTWGTL HPDPAAAKEE

UniProtKB: Uncharacterized protein

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Macromolecule #12: Unknown protein

MacromoleculeName: Unknown protein / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 7.166825 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

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Macromolecule #13: Fucoxanthin chlorophyll a/c-binding protein RedCAP

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein RedCAP / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 23.695039 KDa
SequenceString: MKTAALVTLA LAGSAQAFAP STSRVSVSRT STSVASSVFD DAVKDWAEEY PQFAAWGWGP SVQAEIWNGR HAMFGWVVMC ACAYAKGHG LIPDADQTLD LKEWGTLATI SGKNTITNER AIILIANVHA LMVGLAATIS PNSFADTLLL DPNHPMYEWQ M ERNSKLGG ...String:
MKTAALVTLA LAGSAQAFAP STSRVSVSRT STSVASSVFD DAVKDWAEEY PQFAAWGWGP SVQAEIWNGR HAMFGWVVMC ACAYAKGHG LIPDADQTLD LKEWGTLATI SGKNTITNER AIILIANVHA LMVGLAATIS PNSFADTLLL DPNHPMYEWQ M ERNSKLGG VMPNLGKMGV TPEAELANGR MAMMGIITCI AYSGIQGQSM IDTINEWVGG AYF

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Macromolecule #14: Fucoxanthin chl a/c light-harvesting protein

MacromoleculeName: Fucoxanthin chl a/c light-harvesting protein / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 21.438559 KDa
SequenceString: MLKAVLTTSL IAAASAFAPA SVGRSTVALN EMSKSIPFLT VPEKLDGSMA GDVGFDPMGL SDIQTDLNYA RWAELKHGRI CMLAVVGMV WQEYGPHLPG DAYATKDPWE AISSVGFASN FQTLLAIGVV ELANWNKYYG DGTPGDIGWT GGQLSKMNDA Q IKTRMESE ...String:
MLKAVLTTSL IAAASAFAPA SVGRSTVALN EMSKSIPFLT VPEKLDGSMA GDVGFDPMGL SDIQTDLNYA RWAELKHGRI CMLAVVGMV WQEYGPHLPG DAYATKDPWE AISSVGFASN FQTLLAIGVV ELANWNKYYG DGTPGDIGWT GGQLSKMNDA Q IKTRMESE IVHCRLAMIA FIGATHQTFL LHKGLLDFSY

UniProtKB: Fucoxanthin chl a/c light-harvesting protein

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Macromolecule #15: Pt17531-like protein

MacromoleculeName: Pt17531-like protein / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 21.210223 KDa
SequenceString: MKTAILATLA ASAAAFAPAS ISSPSTTQLS AWRDEVVVGI TAPVGFFDPL GLSKGKDDAT MAYYREAELK NGRVAMAACL GWYLNAGGV HPAFNSELSN DPLKAMVELP AVGWLQFVLG CGAIEWLGQQ IKERPGYVPG DLLGASYWVD NSDEGWVMYQ N KELNNGRL ...String:
MKTAILATLA ASAAAFAPAS ISSPSTTQLS AWRDEVVVGI TAPVGFFDPL GLSKGKDDAT MAYYREAELK NGRVAMAACL GWYLNAGGV HPAFNSELSN DPLKAMVELP AVGWLQFVLG CGAIEWLGQQ IKERPGYVPG DLLGASYWVD NSDEGWVMYQ N KELNNGRL AMLAIVGMVY QDVFVGDYGD MMYKQLVR

UniProtKB: Pt17531-like protein

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Macromolecule #16: Fucoxanthin chl a/c light-harvesting protein, major type

MacromoleculeName: Fucoxanthin chl a/c light-harvesting protein, major type
type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 21.502492 KDa
SequenceString: MKTACLIASS LIASASAFAP APVAKSTTAL SADFSGEIGA ANAELGCWDP LNFCTDQASF DKMRYAELKH GRVAQLAAWG YATTWSGAR FPGCEDFPAG HEAVLKIGTE NLIPVLVVAG ALETLWKQKE GSFPGDFSAT SFPVGFGPFA KTEADMIDLR T KELNNGRA ...String:
MKTACLIASS LIASASAFAP APVAKSTTAL SADFSGEIGA ANAELGCWDP LNFCTDQASF DKMRYAELKH GRVAQLAAWG YATTWSGAR FPGCEDFPAG HEAVLKIGTE NLIPVLVVAG ALETLWKQKE GSFPGDFSAT SFPVGFGPFA KTEADMIDLR T KELNNGRA AMMGILGMIV HEQIDGKPFI FFDKFEIYAP FGN

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

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Macromolecule #17: Fucoxanthin chlorophyll a/c-binding protein Lhcq8

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcq8 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 21.11209 KDa
SequenceString: MKSVCIALLA SSVSAFAPSQ QGPVKSALSY ASELDSMTGT GIESPKVFDP LNLSDYVPVD WARRAELSNG RSAMLATVGW FFPKVFGTF DSTDVTTTDP IDAIMQADPQ WWAQWILICG VFETWKYKKE MEGKSFLGGA DPAVDYLKLW PADAAAQEEM K TKELKNAR ...String:
MKSVCIALLA SSVSAFAPSQ QGPVKSALSY ASELDSMTGT GIESPKVFDP LNLSDYVPVD WARRAELSNG RSAMLATVGW FFPKVFGTF DSTDVTTTDP IDAIMQADPQ WWAQWILICG VFETWKYKKE MEGKSFLGGA DPAVDYLKLW PADAAAQEEM K TKELKNAR LAMIGIAGFA ANHFIPGSCP VPDFIA

UniProtKB: Uncharacterized protein

+
Macromolecule #18: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 18 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #19: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 19 / Number of copies: 138 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #20: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 20 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #21: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 21 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #22: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 22 / Number of copies: 20 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #23: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 23 / Number of copies: 7 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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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: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 25 / Number of copies: 89 / Formula: UNL
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #26: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 26 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #27: Zeaxanthin

MacromoleculeName: Zeaxanthin / type: ligand / ID: 27 / Number of copies: 1 / Formula: 5X6
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-K3I:
Zeaxanthin

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Macromolecule #28: (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: 28 / Number of copies: 7 / 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

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

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

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

+
Macromolecule #30: Chlorophyll c1

MacromoleculeName: Chlorophyll c1 / type: ligand / ID: 30 / Number of copies: 7 / Formula: KC1
Molecular weightTheoretical: 610.941 Da
Chemical component information

ChemComp-KC1:
Chlorophyll c1

+
Macromolecule #31: (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: 31 / Number of copies: 15 / Formula: A86
Molecular weightTheoretical: 658.906 Da

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Macromolecule #32: water

MacromoleculeName: water / type: ligand / ID: 32 / Number of copies: 922 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 6.5
Component:
ConcentrationFormulaName
20.0 mMMES-NaOHMES
0.03 %DDMDDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 60000

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Image processing

Particle selectionNumber selected: 2733572
Startup modelType of model: INSILICO MODEL
In silico model: An initial model was generated de novo from 2D classification.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 75667
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationSoftware - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: ModelAngelo
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-8xls:
PSI-FCPI of the diatom Thalassiosira pseudonana CCMP1335

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