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- EMDB-0835: Structure of the PSI-FCPI supercomplex from diatom -

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Basic information

Entry
Database: EMDB / ID: EMD-0835
TitleStructure of the PSI-FCPI supercomplex from diatom
Map data
Sample
  • Complex: PSI-FCPI
    • Protein or peptide: x 28 types
  • Ligand: x 12 types
KeywordsPhotosystem I / ELECTRON TRANSPORT
Biological speciesChaetoceros gracilis (Diatom)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsNagao R / Kato K
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for assembly and function of a diatom photosystem I-light-harvesting supercomplex.
Authors: Ryo Nagao / Koji Kato / Kentaro Ifuku / Takehiro Suzuki / Minoru Kumazawa / Ikuo Uchiyama / Yasuhiro Kashino / Naoshi Dohmae / Seiji Akimoto / Jian-Ren Shen / Naoyuki Miyazaki / Fusamichi Akita /
Abstract: Photosynthetic light-harvesting complexes (LHCs) play a pivotal role in collecting solar energy for photochemical reactions in photosynthesis. One of the major LHCs are fucoxanthin chlorophyll a/c- ...Photosynthetic light-harvesting complexes (LHCs) play a pivotal role in collecting solar energy for photochemical reactions in photosynthesis. One of the major LHCs are fucoxanthin chlorophyll a/c-binding proteins (FCPs) present in diatoms, a group of organisms having important contribution to the global carbon cycle. Here, we report a 2.40-Å resolution structure of the diatom photosystem I (PSI)-FCPI supercomplex by cryo-electron microscopy. The supercomplex is composed of 16 different FCPI subunits surrounding a monomeric PSI core. Each FCPI subunit showed different protein structures with different pigment contents and binding sites, and they form a complicated pigment-protein network together with the PSI core to harvest and transfer the light energy efficiently. In addition, two unique, previously unidentified subunits were found in the PSI core. The structure provides numerous insights into not only the light-harvesting strategy in diatom PSI-FCPI but also evolutionary dynamics of light harvesters among oxyphototrophs.
History
DepositionOct 21, 2019-
Header (metadata) releaseMay 20, 2020-
Map releaseMay 20, 2020-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6l4u
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0835.png

Downloads & links

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Map

FileDownload / File: emd_0835.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 504 pix.
= 560.952 Å		1.11 Å/pix.
x 504 pix.
= 560.952 Å		1.11 Å/pix.
x 504 pix.
= 560.952 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.113 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.14095047 - 0.4005023
Average (Standard dev.)0.00030691022 (±0.00532834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions504504504
Spacing504504504
CellA=B=C: 560.952 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1131.1131.113
M x/y/z504504504
origin x/y/z0.0000.0000.000
length x/y/z560.952560.952560.952
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS504504504
D min/max/mean-0.1410.4010.000

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Supplemental data

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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: Unknown protein 1
    • Protein or peptide: Photosystem I reaction center subunit Psa28
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr15
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr8
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr2
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr9
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr11
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr12
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr10
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr4
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcf6
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr3
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcq13
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcq3
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcq11
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcq10
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcq8
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcq5
  • 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: 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: Chlorophyll c1
  • Ligand: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
  • Ligand: water

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Supramolecule #1: PSI-FCPI

SupramoleculeName: PSI-FCPI / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#28
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 640 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
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 83.648672 KDa
SequenceString: AISSTERRTK NVQIFVEKDA VETSFEKWAQ PGHFSRTLAK GPKTTTWIWN LHADAHDFDS QTNSLEEVSR KIFSAHFGQL AAIFLWISG MHFHGAYFSN YSAWLSDPIG IKQSSQVVWP IVGQEILNAD VGGNFQGVQT TSGWFQMWRA EGITSEVELY W IAIGGLIM ...String:
AISSTERRTK NVQIFVEKDA VETSFEKWAQ PGHFSRTLAK GPKTTTWIWN LHADAHDFDS QTNSLEEVSR KIFSAHFGQL AAIFLWISG MHFHGAYFSN YSAWLSDPIG IKQSSQVVWP IVGQEILNAD VGGNFQGVQT TSGWFQMWRA EGITSEVELY W IAIGGLIM SALMLFAGWF HYHKAAPKLE WFQNAESMMN HHLAGLLGLG CLSWSGHQIH IALPINKLLD AGVSPQEIPL PH EFLINRE LMAQLYPSFG KGLAPFFSGH WGEYSDFLTF KGGLNPVTGG LWLSDIAHHH LALSVLFIVA GHMYRTNWGI GHS MKEILE AHKGPFTGEG HKGLYEILTT SWHAQLAINL AMMGSLSIIV AHHMYAMPPY PYIATDYATQ LSLFTHHMWI GGFC VTGGA AHAAIFMVRD YTPANNYNNL LDRVLRHRDA IISHLNWVCI FLGCHAFGFY IHNDTMRALG RPQDMFSDKA IQLQP IFAQ WIQNIHLLAP GTTAPNALAT TSYAFGGDVV EVGGKIAMMP IKLGTADFMV HHIHAFTIHV TVLILLKGVL YARSSK LIP DKANLGFRFP CDGPGRGGTC QSSSWDHVFL GLFWMYNSIS VVIFHFSWKM QSDVWGTVTP DGSISHITGG NFAQSSI TI NGWLRDFLWS QASQVIQSYG SASSAYGLIF LGAHFIWAFS LMFLFSGRGY WQELIESIVW AHNKLNFAPA IQPRALSI T QGRAVGLAHY LLGGIGTTWA FFLARSLSIT

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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
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 81.897477 KDa
SequenceString: MATKFPKFSQ ALAQDPATRR IWYGIATAHD LEAHDGMTEE NLYQKIFASH FGHLAIIFLW TAGNLFHVAW QGNFEQWVAK PLKTKPIAH SIWDPHFGES ALKAFSKGNT YPVNIAFSGV YQWWYTIGFR TNQELYAGSI GLLALSCVLL FAGWLHLQPK F RPSLSWFK ...String:
MATKFPKFSQ ALAQDPATRR IWYGIATAHD LEAHDGMTEE NLYQKIFASH FGHLAIIFLW TAGNLFHVAW QGNFEQWVAK PLKTKPIAH SIWDPHFGES ALKAFSKGNT YPVNIAFSGV YQWWYTIGFR TNQELYAGSI GLLALSCVLL FAGWLHLQPK F RPSLSWFK NNESRLNHHL SGLLGVSSLA WTGHIVHVAI PASRGVHVGW DNFLTTPPHP AGLTPFFTGN WTVYAENPDS AS HVYGTSE GAGTAILTFL GGFHPQTQSL WLSDIAHHQL AIAVVFIIAG HMYRTNFGIG HNMKEILDAH RPPGGRLGAG HVG LFETIT NSLHMQLGLA LASLGVATSL TAQHMYALTP YAYLSKDFTT EAALYTHHQY IAGFLMVGAF AHGAIFFVRD YDPE LNKNN VLARMLEHKE AIISHLSWAS LFLGFHTLGL YIHNDTVVAF GQPEKQILFE PVFAEYIQAA SGKAVYQFNV LLSSP TSPA TVAGNQVWLP GWLDAINNPK NDLFLKIGPG DFLVHHAIAL GLHVTALILV KGALDARGSK LMPDKKDFGY SFPCDG PGR GGTCDISAWD AFYLAMFWML NTIGWVTFYW HWKHMTIWGG NPGQFDESSN YIMGWLRDYL WLNSSPLING YNPFGMN NL SVWSWMFLFG HLIWATGFMF LISWRGYWQE LIETLVWAHE RTPLANLIRW RDKPVALSIV QARLVGLAHF SVGYILTY A AFVIASTSGK FG

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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
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 8.807169 KDa
SequenceString:
MSHTVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCKSGQIA SSPRVEDCVG CKRCETACPT DFLSVRVYLG AETTRSLGLA Y

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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: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 15.594646 KDa
SequenceString:
MTLNLQTPFP TFGGSTGGWL RSAEVEEKYA ITWTSKKEQI FEMPTGGAAI MRNGENLLYL ARKEQCLALG TQLRTFKIND YKIYRIFPS GEVQYLHPKD GVFPEKVNPG RTSVNSRDFS IGKNPNPASI KFSGTTTYES

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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: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 7.621467 KDa
SequenceString:
MVGRGSKVRI LRKESYWFNQ VGTVATIDQS GIRYPALVRF ESVNYAGTNS NNFALDELKE VVEETEE

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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: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 20.445615 KDa
SequenceString:
MKRFNILTLL VAVLITLTPN IASAEIGGLT KCSDSPAFAK REKASIKKLE QRKSTYEAGT PPALALQQQI ERTEARFDKY SRSELLCGA DGLPHLIADG RWSHAAEFML PGFGFIYISG WIGWVGRKYL RAVSTTKNPA ESEIIINVPL ALKIMTTGYI W PISAWEEL VSGDLVALDE EVTVSPR

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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: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 3.94474 KDa
SequenceString:
MAAAFLPSIL VPIVGLIFPA FSMALFFLYI QQDDIA

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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: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 4.882824 KDa
SequenceString:
MKNFQKYLST APVLLTIWMT FTAGFIIEIN RFFPDMLGLY F

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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: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 16.148812 KDa
SequenceString:
MANFIKPYND DPFVGHLATP ITSSAVTRAL LKNLPAYRFG LTPLLRGLEI GLAHGYFLIG PFVKLGPLRN SDIALIAGFL STIGLILIL TLGLTIYGAA VFNSDKESLE TTETTLQTRK AWDQFKGGFF VGACGSAGFA LICLSSIPQS IL

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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: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 3.241863 KDa
SequenceString:
MIYDSQVYIA LVIAVVASVL AIRLGATLYN

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Macromolecule #11: Unknown protein 1

MacromoleculeName: Unknown protein 1 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 11.081651 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)(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 #12: Photosystem I reaction center subunit Psa28

MacromoleculeName: Photosystem I reaction center subunit Psa28 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 12.899798 KDa
SequenceString:
FAPMPRAAIS TTQARTASMP SAPFTSLSMA SEDMTWEGEY PPSKVLGPIM SKMPSGLLGL ISIACAAVCA YSIAQSGVLQ QQPGAYENG SWVKWYYVLG SFGGPLAWGT HVASWIQRKN GM

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Macromolecule #13: Fucoxanthin chlorophyll a/c-binding protein Lhcr15

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcr15 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 24.881914 KDa
SequenceString: MILQYFNTFP PPKRSYKKVY NIIIHYFIIM VRSVLLAALV GTAAAFAPAT SMTRRSPAVA LKAEMSESLP FLPRPEKLDG SMAGDRGFD PMGLSEIQQD LTYARWAELK HGRIAMLAIV GMIVQEYIHL PGEAYQNSDP FGAVSTVGLG VNGQIFAAIG C VELINFNK ...String:
MILQYFNTFP PPKRSYKKVY NIIIHYFIIM VRSVLLAALV GTAAAFAPAT SMTRRSPAVA LKAEMSESLP FLPRPEKLDG SMAGDRGFD PMGLSEIQQD LTYARWAELK HGRIAMLAIV GMIVQEYIHL PGEAYQNSDP FGAVSTVGLG VNGQIFAAIG C VELINFNK HYDGSEPGDI GWTGGLLKNK SEAEIMKAKE QEITHCRLAM IAITGATVQT LLFHQPLLG

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Macromolecule #14: Fucoxanthin chlorophyll a/c-binding protein Lhcr8

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcr8 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 21.727959 KDa
SequenceString: MKLALLASLI ASAAAFAPSS STGARASTAL DAGKQSQALP FLPYPENLSG YVGDAGFDPL RFSDYFPMDY LREAEIKHGR ICMLATVGW IAVDMGLRVY PVPAGLEGVT AATAHDASVA QGGLGQVFGW VAVAEMASWI GVSQMLQGSG REPGYFGFDP L GLMKGKSE ...String:
MKLALLASLI ASAAAFAPSS STGARASTAL DAGKQSQALP FLPYPENLSG YVGDAGFDPL RFSDYFPMDY LREAEIKHGR ICMLATVGW IAVDMGLRVY PVPAGLEGVT AATAHDASVA QGGLGQVFGW VAVAEMASWI GVSQMLQGSG REPGYFGFDP L GLMKGKSE AEVNNMKLKE IKNGRLAMLA FSGICTQSVL FDKTFPF

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Macromolecule #15: Fucoxanthin chlorophyll a/c-binding protein Lhcr2

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcr2 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 21.558555 KDa
SequenceString: MKTVAILSLL TASAAAFAPA STTQTSSSTA LAGSVFDNYV GAKDFRGAEF KFDPLKLSET YEPFQGWFRE SELRHGRTAM LAVVGYIAT DFVRIPGEMY SFEAIPKSAD AHDALIASGP MSQLLLWIGL FDLVVTAPAV QAMGKGEREP GDFGLKWFAP S SKDAFDKK ...String:
MKTVAILSLL TASAAAFAPA STTQTSSSTA LAGSVFDNYV GAKDFRGAEF KFDPLKLSET YEPFQGWFRE SELRHGRTAM LAVVGYIAT DFVRIPGEMY SFEAIPKSAD AHDALIASGP MSQLLLWIGL FDLVVTAPAV QAMGKGEREP GDFGLKWFAP S SKDAFDKK REAELLNGRL AMFAIGGIAT QSVLNGHGFP YL

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Macromolecule #16: Fucoxanthin chlorophyll a/c-binding protein Lhcr9

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcr9 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 22.933426 KDa
SequenceString: MAKLSIALTT AAALASSANA FAPSKGARSV TSALSATGFE EVGGKPWDPL SLGKLEDAND TFPNMFPKSQ YLQESEIKHG RMCMLAWTG VWATHVGGMG LGMHIPGMPV ESDWTKALGV FAAEQPALFG AILLFISIAE GESVGHSGDN WRNMSTKEPG N LGFDWMGL ...String:
MAKLSIALTT AAALASSANA FAPSKGARSV TSALSATGFE EVGGKPWDPL SLGKLEDAND TFPNMFPKSQ YLQESEIKHG RMCMLAWTG VWATHVGGMG LGMHIPGMPV ESDWTKALGV FAAEQPALFG AILLFISIAE GESVGHSGDN WRNMSTKEPG N LGFDWMGL TKKLSEEKVA RYKIVELKNG RAAMIAMASL FAMEAIPGSV PIMNVFN

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Macromolecule #17: Fucoxanthin chlorophyll a/c-binding protein Lhcr11

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcr11 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 29.512191 KDa
SequenceString: MVVCHLILSR ITNFLPLSLA HYRTCTSPTP TTPPKKTVVS SALHAEMSKA VPFVKAPANT AGYVGDVGFD PLGFSDYFDM KWLRESEIK HGRASMLACL GFVVQEYITI PGYTHVDDSN LAPQAVGVSA MLQIVLWMGV LEFWTNKGNV TMETMFSSPD R IPGNLGFD ...String:
MVVCHLILSR ITNFLPLSLA HYRTCTSPTP TTPPKKTVVS SALHAEMSKA VPFVKAPANT AGYVGDVGFD PLGFSDYFDM KWLRESEIK HGRASMLACL GFVVQEYITI PGYTHVDDSN LAPQAVGVSA MLQIVLWMGV LEFWTNKGNV TMETMFSSPD R IPGNLGFD PMGLSVGKSQ AEKDEMALKE IKNGRLAMLA IGGMIHHNWR KRHGALTSRE RERNVLQTLD AFLKVHMHTV LC VSCSIWD VNSIFIMRDG IESSFGFPD

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Macromolecule #18: Fucoxanthin chlorophyll a/c-binding protein Lhcr12

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcr12 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 22.362646 KDa
SequenceString: MKLALLASLI ASAAAFAPSS STGAARASTA LDAGKKSQAL PFLPYPENLA GYVGDAGFDP FRFSDFAPMD FLREAEIKHG RICMLAWLG FVAVDLGARI YPLPEAYEGL TAVTAHDALV QQGAMSQIFL WCSVFEAIST VSVIQMLYEE SGREPGYFGF D PLGFLNGK ...String:
MKLALLASLI ASAAAFAPSS STGAARASTA LDAGKKSQAL PFLPYPENLA GYVGDAGFDP FRFSDFAPMD FLREAEIKHG RICMLAWLG FVAVDLGARI YPLPEAYEGL TAVTAHDALV QQGAMSQIFL WCSVFEAIST VSVIQMLYEE SGREPGYFGF D PLGFLNGK SEAEVNEMKL KEIKNGRLAM LAFSGVVTQA VLTQGPFPYV

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Macromolecule #19: Fucoxanthin chlorophyll a/c-binding protein Lhcr10

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcr10 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 32.238152 KDa
SequenceString: LLQGFSRWLV FFVSIRIIRH PCRPPYHETY SSSNTFLSIQ YIEQSHSARQ TSLSLLLITP LTLVLYLAIY TILKMFKTAA AITSLLAAS ASAFAPSSFN GRISTAVAAE KSQSLPFMNR PPLLDGSMAG DVGFDPLGLS NIDDVGIDLY WLREAEIKHC R VAMLAVVG ...String:
LLQGFSRWLV FFVSIRIIRH PCRPPYHETY SSSNTFLSIQ YIEQSHSARQ TSLSLLLITP LTLVLYLAIY TILKMFKTAA AITSLLAAS ASAFAPSSFN GRISTAVAAE KSQSLPFMNR PPLLDGSMAG DVGFDPLGLS NIDDVGIDLY WLREAEIKHC R VAMLAVVG ILQVEIFGPA PGCEMATDKC QMDAFWQIWG AHPQYIAFGL IMIMMIEMIS GIATTQGRES GERAPGDFGL DP LGYGKGD AAGYARLQAQ EIANGRLAMF AAAGEIMQGC TTHQGALENL MTALRDNSF

+
Macromolecule #20: Fucoxanthin chlorophyll a/c-binding protein Lhcr4

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcr4 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 29.70415 KDa
SequenceString: LRSIHHLIAS HRRLFKFIRH YTINKMKSAL IATALLAGSA AAFTSNAGSQ STSALKAMPE RLWDSMVDKT ERSKAVPFLP RAVNLDGSL PGDVGFDPFY LSSIPKDFSG FIQPPQWEEK GIPTLYWMRE AELKHCRVAM LAWFGWLATD GAFGVTLRFP G EIYSVENI ...String:
LRSIHHLIAS HRRLFKFIRH YTINKMKSAL IATALLAGSA AAFTSNAGSQ STSALKAMPE RLWDSMVDKT ERSKAVPFLP RAVNLDGSL PGDVGFDPFY LSSIPKDFSG FIQPPQWEEK GIPTLYWMRE AELKHCRVAM LAWFGWLATD GAFGVTLRFP G EIYSVENI PTAYEAHNAL VSQGSMGFLL LAVGFIEFCT GAVLVEVAKG ASDREAGDFK LDPLSFLKGK SEEEIKRMKT RE IANGRLA MLAFGGVATQ TALEGGNHAF PYF

+
Macromolecule #21: Fucoxanthin chlorophyll a/c-binding protein Lhcf6

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcf6 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 23.517385 KDa
SequenceString: LLLPYSPYLK SSLTHFDISS HSQPPLFSTN PHSSAFAPSS QTNVRSTSSL QAWKDENIIG ITAPMGFFDP LGLSSGKSDE VMNLYREAE LKHGRVAMAA CLGWYITAAG VHPAFNSALS SDPLEAAKQL PTVGWLQFVL GCGAIEWLAQ QIKARPGYQP G DILGAAYW ...String:
LLLPYSPYLK SSLTHFDISS HSQPPLFSTN PHSSAFAPSS QTNVRSTSSL QAWKDENIIG ITAPMGFFDP LGLSSGKSDE VMNLYREAE LKHGRVAMAA CLGWYITAAG VHPAFNSALS SDPLEAAKQL PTVGWLQFVL GCGAIEWLAQ QIKARPGYQP G DILGAAYW VDNSDEGWVD YQNKEINNGR LAMVAFMGIF VQDLYFGNYG DQIFRN

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Macromolecule #22: Fucoxanthin chlorophyll a/c-binding protein Lhcr3

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcr3 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 22.216549 KDa
SequenceString: MKSVAILAAL FGSATAFVPS QVSRTAASTS VKASLADMVG AEGPEPIPFA PSKTSKNFDP VGFAERSPEW LPWYREAELK HGRAAMLAT VGFVVPEFIR VPGEQFSFEA IPKVIDAHDA LPESMIQIFG WISFLEACTF PAMAGLGGKY DRKPGDFSFD P LGLYPTDP ...String:
MKSVAILAAL FGSATAFVPS QVSRTAASTS VKASLADMVG AEGPEPIPFA PSKTSKNFDP VGFAERSPEW LPWYREAELK HGRAAMLAT VGFVVPEFIR VPGEQFSFEA IPKVIDAHDA LPESMIQIFG WISFLEACTF PAMAGLGGKY DRKPGDFSFD P LGLYPTDP EKQKQMQLAE LKNGRLAMIA IGGMVTGAAV TGHGFPYLP

+
Macromolecule #23: Fucoxanthin chlorophyll a/c-binding protein Lhcq13

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcq13 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 24.842496 KDa
SequenceString: MKTAAIFALL AGSAAAFAPT TVSPRASTVA HMSSINEAFG ISIETGNKCP PLGARILEDA QPSAIKWFQN AEIKHGRIAM VATIGYLVQ KLGVHFPLYL GPSGSNCFHP ESETAWLLSS STGVTFSDIA KAAPLDAIQM VPVAGWMQIF FVAGWFESVA Y YRQWVKNS ...String:
MKTAAIFALL AGSAAAFAPT TVSPRASTVA HMSSINEAFG ISIETGNKCP PLGARILEDA QPSAIKWFQN AEIKHGRIAM VATIGYLVQ KLGVHFPLYL GPSGSNCFHP ESETAWLLSS STGVTFSDIA KAAPLDAIQM VPVAGWMQIF FVAGWFESVA Y YRQWVKNS PIPGDYGYDP LGFTKREGGW DSEELTSLRL KEIKNGRLAM MTIAAWVSDE MIPGALPVWH P

+
Macromolecule #24: Fucoxanthin chlorophyll a/c-binding protein Lhcq3

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcq3 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 21.318404 KDa
SequenceString: MKSVLFLALA GSAAAFAPST QSRSNTLLKA DLSSLPGSTA PVGPFDPLNL ADSGSEETLA WFRASELKHG RVAMLATTGY LVQGAGIHF PGMLSSDVSF ESLSAMKPLE AWDAVPDAGK AQILGTIFIA EMITESKPVH YTKGGPMPTM VFPAIDFSGV D AATLKRKQ ...String:
MKSVLFLALA GSAAAFAPST QSRSNTLLKA DLSSLPGSTA PVGPFDPLNL ADSGSEETLA WFRASELKHG RVAMLATTGY LVQGAGIHF PGMLSSDVSF ESLSAMKPLE AWDAVPDAGK AQILGTIFIA EMITESKPVH YTKGGPMPTM VFPAIDFSGV D AATLKRKQ DSELNNGRLA MIAIMSFISA ANIPGSVPAL TNNPAF

+
Macromolecule #25: Fucoxanthin chlorophyll a/c-binding protein Lhcq11

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcq11 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 25.994562 KDa
SequenceString: MKLAILTTLL AGASAFTTPN ARPAFATKLS MSEEAAAEEA PAADAPEEVV EPASPSYTCI SKEAILSSPD TTEIGRVWDP LGLAEIGSA ETLAWYRHSE VKHGRIAMAA FVGWWAVGAG LRFPGELSHG LEFSSIPSKG LEAWDAVPGW GKAQMLLFAG L IEFHDELF ...String:
MKLAILTTLL AGASAFTTPN ARPAFATKLS MSEEAAAEEA PAADAPEEVV EPASPSYTCI SKEAILSSPD TTEIGRVWDP LGLAEIGSA ETLAWYRHSE VKHGRIAMAA FVGWWAVGAG LRFPGELSHG LEFSSIPSKG LEAWDAVPGW GKAQMLLFAG L IEFHDELF HTRRTEGGHY LRGGTPGKNM VPGLFDPFGF SKGKSEEELA KGRDREIKNG RLAMIGVAGL YCAATIPGSV PL QPPC

+
Macromolecule #26: Fucoxanthin chlorophyll a/c-binding protein Lhcq10

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcq10 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 26.875781 KDa
SequenceString: MKIILSGLAL LASSVAAFAP QSIISANANN KNANVVLEAA KDDLIAIAEK SNPVLKYYDP LQLGSTTIWG ETNSATIGFL RQSEIKHGR IAMAAFVGYI VQANGIHFPW PMSFDGTPFP ADAGSPPEQW DALSDAAKWQ IILFIGFLEW FSEAAGKHYM R GGKPGAFP ...String:
MKIILSGLAL LASSVAAFAP QSIISANANN KNANVVLEAA KDDLIAIAEK SNPVLKYYDP LQLGSTTIWG ETNSATIGFL RQSEIKHGR IAMAAFVGYI VQANGIHFPW PMSFDGTPFP ADAGSPPEQW DALSDAAKWQ IILFIGFLEW FSEAAGKHYM R GGKPGAFP NFSDSDLIPH PVPLNLYDPF GFSKGKTEAQ KADGLIKELN NGRLAMIGIM GFLAEQKVEG SVPLLKGVVP HY DGEVMAP FM

+
Macromolecule #27: Fucoxanthin chlorophyll a/c-binding protein Lhcq8

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcq8 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 30.545674 KDa
SequenceString: MDNKIAGYNI IIHTIISSIN MKFSLVVLSS LVVASSNGVT AFAPSSSTTS TSTTALSSSA SKAELEAIAK KANPTLGYYD PLSLADKDF WGKGNDATIA FLRQSEIKHG RIAMFAFVGY IVQSNFVFPW AQTLAGAPHP SADLSPEAQW DAIPLGAKWQ I FAVISALE ...String:
MDNKIAGYNI IIHTIISSIN MKFSLVVLSS LVVASSNGVT AFAPSSSTTS TSTTALSSSA SKAELEAIAK KANPTLGYYD PLSLADKDF WGKGNDATIA FLRQSEIKHG RIAMFAFVGY IVQSNFVFPW AQTLAGAPHP SADLSPEAQW DAIPLGAKWQ I FAVISALE LWDECGGGGV LPHYTKGRKP GQYPPFTLFR DNVHFVLDLY DPFGFNKNMS EETKERRLVS ELNNGRLAML GI FGFLCAD TIPGSVPLLN DIAIPYSGQV MQPFEGQFSY FGSL

+
Macromolecule #28: Fucoxanthin chlorophyll a/c-binding protein Lhcq5

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcq5 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 23.533191 KDa
SequenceString: MKIATLFLAL ASSAAAFAPS QQVRSMTNEK MKPRQARNNF ALNMKVDEMP GATAPLGKFD PLNLATLGSE STLAWFRAAE LKHSRVAML ATTGYLVQAA GIHFPGMLSS DVSFESLSAM KPLDAWDAVP EGGKNQIYFT IFLAEFITEC KGTHYTKGGP L PTIVFPPI ...String:
MKIATLFLAL ASSAAAFAPS QQVRSMTNEK MKPRQARNNF ALNMKVDEMP GATAPLGKFD PLNLATLGSE STLAWFRAAE LKHSRVAML ATTGYLVQAA GIHFPGMLSS DVSFESLSAM KPLDAWDAVP EGGKNQIYFT IFLAEFITEC KGTHYTKGGP L PTIVFPPI DFSTVNPEQL KTRQNRELNN GRLAMIAIMS FVAAANIPGS VPALAGNPMF

+
Macromolecule #29: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 29 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

+
Macromolecule #30: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 30 / Number of copies: 221 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #31: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 31 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

+
Macromolecule #32: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 32 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

+
Macromolecule #33: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 33 / Number of copies: 20 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #34: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 34 / Number of copies: 7 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #35: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 35 / Number of copies: 21 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

+
Macromolecule #36: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 36 / Number of copies: 13 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #37: (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: 37 / Number of copies: 54 / Formula: A86
Molecular weightTheoretical: 658.906 Da

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Macromolecule #38: Chlorophyll c1

MacromoleculeName: Chlorophyll c1 / type: ligand / ID: 38 / Number of copies: 54 / Formula: KC1
Molecular weightTheoretical: 610.941 Da
Chemical component information

ChemComp-KC1:
Chlorophyll c1

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Macromolecule #39: (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: 39 / Number of copies: 31 / 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 #40: water

MacromoleculeName: water / type: ligand / ID: 40 / Number of copies: 156 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
20.0 mMMES-NaOHMES-NaOH
0.02 %DDMDDM
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2689965
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

9853

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 470801
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

PDB-6l4u:
Structure of the PSI-FCPI supercomplex from diatom

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