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- EMDB-62499: PSII-FCPII supercomplex from haptophyte Chrysotila roscoffensis -

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Basic information

Entry
Database: EMDB / ID: EMD-62499
TitlePSII-FCPII supercomplex from haptophyte Chrysotila roscoffensis
Map dataCryo-EM map of a PSII-FCPII supercomplex from haptophyte Chrysotila roscoffensis.
Sample
  • Complex: Photosystem II (PSII)-fucoxanthin chlorophyll a/c binding protein II (FCPII) supercomplex from haptophyte Chrysotila roscoffensis
    • Protein or peptide: x 10 types
  • Protein or peptide: x 10 types
  • Ligand: x 16 types
Keywordsphotosystem II / photosynthesis / chlorophyll / light-harvesting complex / energy transfer / LHCII / FCPII / coccolithophore / haptophyte
Function / homology
Function and homology information


thylakoid membrane / photosynthesis, light harvesting / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / photosystem II / response to herbicide / chlorophyll binding / photosynthetic electron transport in photosystem II / : ...thylakoid membrane / photosynthesis, light harvesting / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / photosystem II / response to herbicide / chlorophyll binding / photosynthetic electron transport in photosystem II / : / chloroplast thylakoid membrane / photosynthesis / chloroplast / electron transfer activity / oxidoreductase activity / iron ion binding / heme binding / metal ion binding / membrane
Similarity search - Function
Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II CP43 reaction centre protein / Photosystem II CP43 reaction centre protein superfamily / Photosystem II CP47 reaction centre protein / Photosystem II protein D1 ...Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II CP43 reaction centre protein / Photosystem II CP43 reaction centre protein superfamily / Photosystem II CP47 reaction centre protein / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Chlorophyll A-B binding protein, plant and chromista / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Photosystem II CP43 reaction center protein / Photosystem II reaction center protein T / Light harvesting protein / Photosystem II protein D1 / H(+)-exporting diphosphatase / Photosystem II reaction center protein L / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II D2 protein / Photosystem II CP47 reaction center protein
Similarity search - Component
Biological speciesChrysotila roscoffensis (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.22 Å
AuthorsLa Rocca R / Kato K / Tsai P-C / Nakajima Y / Akita F / Shen J-R
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Structure of a photosystem II-FCPII supercomplex from a haptophyte reveals a distinct antenna organization.
Authors: Romain La Rocca / Koji Kato / Pi-Cheng Tsai / Yoshiki Nakajima / Fusamichi Akita / Jian-Ren Shen /
Abstract: Haptophytes are unicellular algae that produce 30 to 50% of biomass in oceans. Among haptophytes, a subset named coccolithophores is characterized by calcified scales. Despite the importance of ...Haptophytes are unicellular algae that produce 30 to 50% of biomass in oceans. Among haptophytes, a subset named coccolithophores is characterized by calcified scales. Despite the importance of coccolithophores in global carbon fixation and CaCO production, their energy conversion system is still poorly known. Here we report a cryo-electron microscopic structure of photosystem II (PSII)-fucoxanthin chlorophyll c-binding protein (FCPII) supercomplex from Chyrostila roscoffensis, a representative of coccolithophores. This complex has two sets of six dimeric and monomeric FCPIIs, with distinct orientations. Interfaces of both FCPII/FCPII and FCPII/core differ from previously reported. We also determine the sequence of Psb36, a subunit previously found in diatoms and red algae. The principal excitation energy transfer (EET) pathways involve mainly 5 FCPIIs, where one FCPII monomer mediates EET to CP47. Our findings provide a solid structural basis for EET and energy dissipation pathways occurring in coccolithophores.
History
DepositionNov 25, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62499.png

Downloads & links

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Map

FileDownload / File: emd_62499.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of a PSII-FCPII supercomplex from haptophyte Chrysotila roscoffensis.
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 600 pix.
= 436.2 Å		0.73 Å/pix.
x 600 pix.
= 436.2 Å		0.73 Å/pix.
x 600 pix.
= 436.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.10989528 - 0.29804572
Average (Standard dev.)0.00009293009 (±0.0072639408)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 436.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62499_msk_1.map
Projections & Slices
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Half map: Half map (A).

Fileemd_62499_half_map_1.map
AnnotationHalf map (A).
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: Half map (B).

Fileemd_62499_half_map_2.map
AnnotationHalf map (B).
Projections & Slices
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Slices (1/2)
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Sample components

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Entire : Photosystem II (PSII)-fucoxanthin chlorophyll a/c binding protein...

EntireName: Photosystem II (PSII)-fucoxanthin chlorophyll a/c binding protein II (FCPII) supercomplex from haptophyte Chrysotila roscoffensis
Components
  • Complex: Photosystem II (PSII)-fucoxanthin chlorophyll a/c binding protein II (FCPII) supercomplex from haptophyte Chrysotila roscoffensis
    • Protein or peptide: Cytochrome b559 subunit alpha
    • Protein or peptide: Cytochrome b559 subunit beta
    • Protein or peptide: Photosystem II reaction center protein H (psbH)
    • Protein or peptide: Photosystem II reaction center protein I (psbI)
    • Protein or peptide: Photosystem II reaction center protein K (psbK)
    • Protein or peptide: Photosystem II reaction center protein L
    • Protein or peptide: Photosystem II reaction center protein M (psbM)
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: Photosystem II reaction center protein W (psbW)
    • Protein or peptide: Photosystem II reaction center protein X (psbX)
  • Protein or peptide: Fucoxanthin chlorophyll a/c binding protein II (FCPII-1)
  • Protein or peptide: Fucoxanthin chlorophyll a/c binding protein II (FCPII-5)
  • Protein or peptide: Photosystem II protein D1
  • Protein or peptide: Photosystem II CP47 reaction center protein
  • Protein or peptide: Photosystem II reaction center protein Psb36
  • Protein or peptide: Fucoxanthin chlorophyll a/c binding protein II (FCPII-2)
  • Protein or peptide: Photosystem II D2 protein
  • Protein or peptide: Photosystem II CP43 reaction center protein
  • Protein or peptide: Light harvesting protein
  • Protein or peptide: Fucoxanthin chlorophyll a/c binding protein II (FCPII-4)
  • Ligand: CHLOROPHYLL A
  • Ligand: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
  • 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: BETA-CAROTENE
  • Ligand: PHEOPHYTIN A
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: BICARBONATE ION
  • Ligand: FE (II) ION
  • Ligand: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
  • Ligand: water

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Supramolecule #1: Photosystem II (PSII)-fucoxanthin chlorophyll a/c binding protein...

SupramoleculeName: Photosystem II (PSII)-fucoxanthin chlorophyll a/c binding protein II (FCPII) supercomplex from haptophyte Chrysotila roscoffensis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #5-#11, #13-#15
Details: PSII-FCPII supercomplex containing two sets of 6 symmetrical FCPII.
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)

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Macromolecule #1: Fucoxanthin chlorophyll a/c binding protein II (FCPII-1)

MacromoleculeName: Fucoxanthin chlorophyll a/c binding protein II (FCPII-1)
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 18.30784 KDa
SequenceString:
MGYENELGVI EPTGFFDPLG LSANIDEETF AQYRTAELKH GRVAQLCVIG YVVPEIYRFP GEIAPGVAFA DIPNGVAAIN AIPSLGWLQ MIFFIGAVDY WGVLGDFDIG KPKLDPDELE KRQVQELQHG RLAMIATLEL LRHDSQNLVT PGFDGLDTLI T GLPFLY

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Macromolecule #2: Fucoxanthin chlorophyll a/c binding protein II (FCPII-5)

MacromoleculeName: Fucoxanthin chlorophyll a/c binding protein II (FCPII-5)
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 18.451154 KDa
SequenceString:
MGYETELGVI PPTGFFDPLG LSKNIDEETF AQYRTAELKH GRVAQLCVIG YVVPEFYRFP GIIAPGVPFA DIPNGVAAIN AIPALGWFQ MVFLIGAVDY WGVLGDFDAG KPDLAPEELE KRKLQELQHG RLAMLAVLEL LRHDSQNLVK PGFDGLDNLI T GFPFLYN

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Macromolecule #3: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 39.588004 KDa
SequenceString: MTTTLERRES ASFWEQFCAW ITSTENRLYI GWFGCLMFPT LLTATSAYII AFIAAPPVDI DGIREPVAGS LLYGNNIISG AVVPSSNAI GVHFYPIWEA ASIDEWLYNG GPYQLVVFHF FIGVCAYIGR EWELSYRLGM RPWICVAFSA PVAAAAAVFV I YPIGQGSF ...String:
MTTTLERRES ASFWEQFCAW ITSTENRLYI GWFGCLMFPT LLTATSAYII AFIAAPPVDI DGIREPVAGS LLYGNNIISG AVVPSSNAI GVHFYPIWEA ASIDEWLYNG GPYQLVVFHF FIGVCAYIGR EWELSYRLGM RPWICVAFSA PVAAAAAVFV I YPIGQGSF SDGMPLGISG TFNFMLVFQA EHNILMHPFH MLGVAGVFGG SLFSAMHGSL VTSSLIRETS ENESLNYGYK FG QEEETYN IVAAHGYFGR LIFQYASFNN SRALHFFLGA WPVVGIWFTA MGVATMAFNL NGFNFNQSVV DSQGRVINTW ADI LNRSNL GMEVMHERNA HNFPLDLAAG ESLPVALVAP AVAA

UniProtKB: Photosystem II protein D1

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Macromolecule #4: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 56.32425 KDa
SequenceString: MALPWYRVHT VVLNDPGRLI AVHLMHTALV AGWAGSMALY ELAVFDPSDP VLNPMWRQGM FVMPFMARLG VTDSWGGWSI TGESVSNPG IWSFEGVALT HIVLSGLCFL AAIWHWVYWD LELFRDPRTG EPALDLPKIF GIHLFLASLL CFGFGAFHVT G AFGPGIWV ...String:
MALPWYRVHT VVLNDPGRLI AVHLMHTALV AGWAGSMALY ELAVFDPSDP VLNPMWRQGM FVMPFMARLG VTDSWGGWSI TGESVSNPG IWSFEGVALT HIVLSGLCFL AAIWHWVYWD LELFRDPRTG EPALDLPKIF GIHLFLASLL CFGFGAFHVT G AFGPGIWV SDAYGVTGRV QAVAPAWGPE GFNPFNPGGI ASHHIAAGIL GILAGVFHLT IRPPQRLYRA LRMGNIETVL SS SISAVFF AAFITSGTMW YGAATTPIEL FGPTRYQWDS GYFQQEIERR VEASISEGLS LSQAWSRIPD KLAFYDYIGN NPA KGGLFR AGPMNKGDGI AEAWLGHPVF QDKEGRELTV RRMPAFFETF PVILVDKDGI VRADIPFRRA ESKYSIEQVG VSCN FYGGK LNGQVFTDAP TVKKYARKSQ LGEVFEFDRT TLESDGVFRS SPRGWYTFGH ANFALLFFLG HLWHGGRTLF RDVFA GIGA EVLEQVEFGA FQKLGDKSTK KQGIV

UniProtKB: Photosystem II CP47 reaction center protein

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Macromolecule #5: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 9.22033 KDa
SequenceString:
GGSTGERPFS DIITSIRYWI IHSITIPSLF VAGFLFVSTG LAYDAFGTPR PNEYFTQDRQ QIPLVNDRFS AKQELEDLTK GL

UniProtKB: Cytochrome b559 subunit alpha

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Macromolecule #6: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 4.858744 KDa
SequenceString:
MINTNQPVAY PIFTFRWLTI HALAVPTVFF LGAITSMQFI QR

UniProtKB: Cytochrome b559 subunit beta

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Macromolecule #7: Photosystem II reaction center protein H (psbH)

MacromoleculeName: Photosystem II reaction center protein H (psbH) / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 7.259597 KDa
SequenceString:
MALRTRLGEI LRPLNAEYGK VAPGWGTTSV MGVFMALFLV FLVIILQIYN SSIILENVDV DWVTV

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Macromolecule #8: Photosystem II reaction center protein I (psbI)

MacromoleculeName: Photosystem II reaction center protein I (psbI) / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 4.461228 KDa
SequenceString:
MFTLKILVYT VVIFFISLFT FGFLSSDPSR NPNRKDLE

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Macromolecule #9: Photosystem II reaction center protein K (psbK)

MacromoleculeName: Photosystem II reaction center protein K (psbK) / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 4.461356 KDa
SequenceString:
LLSALPEPYT AFRPIVDVMP AIPVLFLLLA FVWQASVGFR

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Macromolecule #10: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 4.393113 KDa
SequenceString:
MSAPNPNKQP VELNRTSLYW GLLLIFVLAV LFSSYFFN

UniProtKB: Photosystem II reaction center protein L

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Macromolecule #11: Photosystem II reaction center protein M (psbM)

MacromoleculeName: Photosystem II reaction center protein M (psbM) / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 13.414595 KDa
SequenceString:
LCIGRSAAAA MKLTLAFACL AAVEAFVQQP ALRPMQSKMA VSKLASSPSM SLETSSIAQL SETLAGVVAV DGGTIGLEVS FGAFLAVIL GLFIPVVFLV TLYIQSEAQG TATNFRLPDK APGVPGDRYD A

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Macromolecule #12: Photosystem II reaction center protein Psb36

MacromoleculeName: Photosystem II reaction center protein Psb36 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 3.458977 KDa
SequenceString:
MAVASNAGDF GGYTIPIIGL GLIGATIALL AGPVDE

UniProtKB: H(+)-exporting diphosphatase

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Macromolecule #13: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 3.77666 KDa
SequenceString:
MEALVYTFLL IGTLIVIFFA IFFRDPPRIV KK

UniProtKB: Photosystem II reaction center protein T

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Macromolecule #14: Photosystem II reaction center protein W (psbW)

MacromoleculeName: Photosystem II reaction center protein W (psbW) / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 5.643089 KDa
SequenceString:
GTGKALGIND DSLGFVLIGV TAVIGLAWAQ WQSYQDDGDD FFDTYDSRRA AAA

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Macromolecule #15: Photosystem II reaction center protein X (psbX)

MacromoleculeName: Photosystem II reaction center protein X (psbX) / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 3.674456 KDa
SequenceString:
MTPSLSAFLS SVILAVVIIV IPIGAALVFV STSDKI

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Macromolecule #16: Fucoxanthin chlorophyll a/c binding protein II (FCPII-2)

MacromoleculeName: Fucoxanthin chlorophyll a/c binding protein II (FCPII-2)
type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 24.920742 KDa
SequenceString: MKAPPPKAKG RGWLQKARIA DEIDVTGSQY VNVAGLTPQY DEIGVLPPLG RWDPLNIKGQ GEARYRRFVE MEIKHGRMAM AAVLGVLTT YSGIRFPGYL SKTLDLKFED VPGTMIGSWA TVPVTGWIQI VLFVVLLEAS WWKQDPAKAP GDVVPEGVWW A RYPDGYSI ...String:
MKAPPPKAKG RGWLQKARIA DEIDVTGSQY VNVAGLTPQY DEIGVLPPLG RWDPLNIKGQ GEARYRRFVE MEIKHGRMAM AAVLGVLTT YSGIRFPGYL SKTLDLKFED VPGTMIGSWA TVPVTGWIQI VLFVVLLEAS WWKQDPAKAP GDVVPEGVWW A RYPDGYSI FLGDGSVKTV AEDELFLGKT WKLNAERNNG RAAMMGITGM YVHELLTGNP VYPLGEL

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Macromolecule #17: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 39.143762 KDa
SequenceString: MTIAIGQKQD RGVFDLIDDW LKRDRFVFVG WSGLLLFPCA FLAVGGWLTG ITFVTSWYTH GLASSFLEGC NFLTAAVSTP ANSMGHSLL LLWGPEAQGD ITRWFQIGGL WTFVALHGSF GVIGFCLRQF EIARLVGIRP YNAIAFSGPI AVFVTVFLVY P LGQASWFF ...String:
MTIAIGQKQD RGVFDLIDDW LKRDRFVFVG WSGLLLFPCA FLAVGGWLTG ITFVTSWYTH GLASSFLEGC NFLTAAVSTP ANSMGHSLL LLWGPEAQGD ITRWFQIGGL WTFVALHGSF GVIGFCLRQF EIARLVGIRP YNAIAFSGPI AVFVTVFLVY P LGQASWFF APSFGVAAIF RFLLFLQGFH NWTLNPFHMM GVAGILGGAL LCAIHGATVE NTLFEDGDAA NTFRAFTPTQ SE ETYSMVT ANRFWSQIFG VAFSNKRWLH FFMLFVPVAG MWTSSLGIVG LALNLRSYDF VSQELRAAED PEFETFYTKN NLL NEGIRS WMAAQDQPHE NFIFPEEVLP RGNAL

UniProtKB: Photosystem II D2 protein

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Macromolecule #18: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 48.73373 KDa
SequenceString: ESTGFAWWSG NARLINVSGK LLGAHVAHAG LMVFWCGAMT LFEVAHYIPE KPLYEQGCIL IPHLTTLGWG VGPGGEVTDV YPFFVVGVL HLISSAVLGF GGVYHSLIGP DTLEESFPFF GYDWRDKNKM TTILGIHLIL LGIGSFLLVA KACFVGGLYD T WAPGGGDV ...String:
ESTGFAWWSG NARLINVSGK LLGAHVAHAG LMVFWCGAMT LFEVAHYIPE KPLYEQGCIL IPHLTTLGWG VGPGGEVTDV YPFFVVGVL HLISSAVLGF GGVYHSLIGP DTLEESFPFF GYDWRDKNKM TTILGIHLIL LGIGSFLLVA KACFVGGLYD T WAPGGGDV RIVTAPTLNP LIIFGYVLKS PFGGDGWIIS VNNLEDLVGG HIWLGFLCVV GGIWHILTKP FAWARRTFVW SG EAYLSYS LAALSVMGLT ASVFVWYNNT AYPSEFFGPT GPEASQSQAF TFLVRDQRLG ANVASAQGPT GLGKYLMRSP SGE IIFGGE TMRFWDMRAP WVEPLRGPNG LDLNKIRNDI QPWQERRAAE YMTHAPLGAL NSVGGVATEI NSVNYVSPRS WLTT SHFFL GFFLWVGHLW HAGRARAAAA GFEKGINREN EPVLSMRPLD

UniProtKB: Photosystem II CP43 reaction center protein

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Macromolecule #19: Light harvesting protein

MacromoleculeName: Light harvesting protein / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 23.662523 KDa
SequenceString: MTPETICLLL ADVVKMISVV LGSLAFNGLV TPAPTRAAVS MSAISPGDIG TTRPLGVFDP LKLMEKNPGK YRRFQEMEIK HGRIAMLAT LHVFITGAGY KWPGYCSYLS FPPLKFEDIP AGTLASWAAL PQAGWAQIVA VVAILDNSLF AQDPNREPGD V AGDLPWVR ...String:
MTPETICLLL ADVVKMISVV LGSLAFNGLV TPAPTRAAVS MSAISPGDIG TTRPLGVFDP LKLMEKNPGK YRRFQEMEIK HGRIAMLAT LHVFITGAGY KWPGYCSYLS FPPLKFEDIP AGTLASWAAL PQAGWAQIVA VVAILDNSLF AQDPNREPGD V AGDLPWVR YDDPKVKEYK LNIERNNGRA AMMGIIGMMT HEYLTGNPLY PLSYEPVV

UniProtKB: Light harvesting protein

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Macromolecule #20: Fucoxanthin chlorophyll a/c binding protein II (FCPII-4)

MacromoleculeName: Fucoxanthin chlorophyll a/c binding protein II (FCPII-4)
type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 18.438115 KDa
SequenceString:
MSYESELGVI PPTGFFDPLG LSKNIDEETF AQYRTAELKH GRVAQLCVIG YIVPEIYRFP GEIAPGVAFA DIPNGVAAIN AIPALGWFQ MVFLIGAVDY WGFLGDFEAG KPDLAPEELE KRKLQELQHG RLAMLAVLEL LRHDSQNLVS PGFDGLDKLI T GLPFLYN

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Macromolecule #21: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 21 / Number of copies: 156 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #22: (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: 22 / Number of copies: 4 / 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 #23: (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: 23 / Number of copies: 28 / Formula: A86
Molecular weightTheoretical: 658.906 Da

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Macromolecule #24: Chlorophyll c1

MacromoleculeName: Chlorophyll c1 / type: ligand / ID: 24 / Number of copies: 36 / Formula: KC1
Molecular weightTheoretical: 610.941 Da
Chemical component information

ChemComp-KC1:
Chlorophyll c1

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Macromolecule #25: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 25 / Number of copies: 18 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #26: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 26 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #27: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 27 / Number of copies: 8 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #28: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 28 / Number of copies: 21 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #29: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 29 / Number of copies: 9 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMU:
DODECYL-ALPHA-D-MALTOSIDE / detergent*YM

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Macromolecule #30: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 30 / Number of copies: 8 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #31: 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: 31 / Number of copies: 5 / 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 #32: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 32 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #33: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 33 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION

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Macromolecule #34: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 34 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #35: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...

MacromoleculeName: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
type: ligand / ID: 35 / Number of copies: 2 / Formula: PL9
Molecular weightTheoretical: 749.201 Da
Chemical component information

ChemComp-PL9:
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE

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Macromolecule #36: water

MacromoleculeName: water / type: ligand / ID: 36 / Number of copies: 181 / 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

Concentration1.53 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
50.0 mMNaClsodium chloride
0.05 %alpha-DDMn-Dodecyl alpha-maltoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Pressure: 0.007 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: Light was turned off during the blot..

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / 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: 0.8 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio reconstruction
Final reconstructionNumber classes used: 12 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38582
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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