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- EMDB-36366: Cryo-EM structure of Symbiodinium photosystem I -

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Basic information

Entry
Database: EMDB / ID: EMD-36366
TitleCryo-EM structure of Symbiodinium photosystem I
Map dataCryo-EM structure of Symbiodinium photosystem I
Sample
  • Complex: Photosystem I of Symbiodinium
    • Protein or peptide: x 26 types
  • Ligand: x 13 types
KeywordsSymbiodinium / Photosystem I / PHOTOSYNTHESIS
Biological speciesSymbiodinium sp. (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsZhao LS / Wang N / Li K / Zhang YZ / Liu LN
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Commun / Year: 2024
Title: Architecture of symbiotic dinoflagellate photosystem I-light-harvesting supercomplex in Symbiodinium.
Authors: Long-Sheng Zhao / Ning Wang / Kang Li / Chun-Yang Li / Jian-Ping Guo / Fei-Yu He / Gui-Ming Liu / Xiu-Lan Chen / Jun Gao / Lu-Ning Liu / Yu-Zhong Zhang /
Abstract: Symbiodinium are the photosynthetic endosymbionts for corals and play a vital role in supplying their coral hosts with photosynthetic products, forming the nutritional foundation for high-yield coral ...Symbiodinium are the photosynthetic endosymbionts for corals and play a vital role in supplying their coral hosts with photosynthetic products, forming the nutritional foundation for high-yield coral reef ecosystems. Here, we determine the cryo-electron microscopy structure of Symbiodinium photosystem I (PSI) supercomplex with a PSI core composed of 13 subunits including 2 previously unidentified subunits, PsaT and PsaU, as well as 13 peridinin-Chl a/c-binding light-harvesting antenna proteins (AcpPCIs). The PSI-AcpPCI supercomplex exhibits distinctive structural features compared to their red lineage counterparts, including extended termini of PsaD/E/I/J/L/M/R and AcpPCI-1/3/5/7/8/11 subunits, conformational changes in the surface loops of PsaA and PsaB subunits, facilitating the association between the PSI core and peripheral antennae. Structural analysis and computational calculation of excitation energy transfer rates unravel specific pigment networks in Symbiodinium PSI-AcpPCI for efficient excitation energy transfer. Overall, this study provides a structural basis for deciphering the mechanisms governing light harvesting and energy transfer in Symbiodinium PSI-AcpPCI supercomplexes adapted to their symbiotic ecosystem, as well as insights into the evolutionary diversity of PSI-LHCI among various photosynthetic organisms.
History
DepositionMay 31, 2023-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36366.png

Downloads & links

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Map

FileDownload / File: emd_36366.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Symbiodinium photosystem I
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.098823845 - 2.9602902
Average (Standard dev.)0.041333348 (±0.08881352)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of Symbiodinium photosystem I

Fileemd_36366_half_map_1.map
AnnotationCryo-EM structure of Symbiodinium photosystem I
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of Symbiodinium photosystem I

Fileemd_36366_half_map_2.map
AnnotationCryo-EM structure of Symbiodinium photosystem I
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Photosystem I of Symbiodinium

EntireName: Photosystem I of Symbiodinium
Components
  • Complex: Photosystem I of Symbiodinium
    • Protein or peptide: PCPI-7
    • Protein or peptide: PCPI-1
    • Protein or peptide: PCP-11
    • Protein or peptide: PCPI-6
    • Protein or peptide: PCPI-5
    • Protein or peptide: PCPI-8
    • Protein or peptide: PCPI-4
    • Protein or peptide: PCPI-10
    • Protein or peptide: PCPI-3
    • Protein or peptide: PCPI-9
    • Protein or peptide: PCPI-13
    • Protein or peptide: PCPI-12
    • Protein or peptide: PCPI-2
    • Protein or peptide: PsaA
    • Protein or peptide: PsaB
    • Protein or peptide: PsaC
    • Protein or peptide: PsaD
    • Protein or peptide: PsaE
    • Protein or peptide: PsaF
    • Protein or peptide: PsaI
    • Protein or peptide: PsaJ
    • Protein or peptide: PsaL
    • Protein or peptide: PsaM
    • Protein or peptide: PsaR
    • Protein or peptide: PsaT
    • Protein or peptide: PsaU
  • Ligand: CHLOROPHYLL A
  • Ligand: Chlorophyll c2
  • Ligand: [(1~{S},5~{R})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl] ethanoate
  • 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-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: PERIDININ
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: PHYLLOQUINONE
  • Ligand: BETA-CAROTENE
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: Photosystem I of Symbiodinium

SupramoleculeName: Photosystem I of Symbiodinium / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#26
Source (natural)Organism: Symbiodinium sp. (eukaryote)

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Macromolecule #1: PCPI-7

MacromoleculeName: PCPI-7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 27.129824 KDa
SequenceString: MLAYGGIVTT AVLTQEKWPF FDAVVNAVPD NKQVRAPATF CGGAAPRSVS RTACHASSSK SLPFLPKPQN LGGLAGGDAE FDPLGFSDT FDVKWLRESE LKHGRVCMLA TVGFVAEQYI QFPGFTPAED ALQAIYTAPP NITALLLFAC GYIESSAYDG K LTMLDMFD ...String:
MLAYGGIVTT AVLTQEKWPF FDAVVNAVPD NKQVRAPATF CGGAAPRSVS RTACHASSSK SLPFLPKPQN LGGLAGGDAE FDPLGFSDT FDVKWLRESE LKHGRVCMLA TVGFVAEQYI QFPGFTPAED ALQAIYTAPP NITALLLFAC GYIESSAYDG K LTMLDMFD GEGAKRAPGD LNFGKRFLPG DKAAADDLAT KELSNGRLAM LAFAGMVHHN LVVKGPLFPL FPEGWAGPQG SW DLDSTAG ALNSGSLGL

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Macromolecule #2: PCPI-1

MacromoleculeName: PCPI-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 28.182102 KDa
SequenceString: MARVAALALS AGGLAFVVPR SSTSTSSLRG VSVSAPAAEP TSSASWGAAA ATATAALGLA AASATSATRR TARKAVGVCL PLTDKFDPL NLASTDEKLE RYTQVEIKHG RVAMIAVVGY IMPEIFRFPG CESFQHGLAA LESIPLEGWV QLAALVGAHE V LVKPRAGG ...String:
MARVAALALS AGGLAFVVPR SSTSTSSLRG VSVSAPAAEP TSSASWGAAA ATATAALGLA AASATSATRR TARKAVGVCL PLTDKFDPL NLASTDEKLE RYTQVEIKHG RVAMIAVVGY IMPEIFRFPG CESFQHGLAA LESIPLEGWV QLAALVGAHE V LVKPRAGG LGTSDFGLGT ELLDGIEEPE LERKLTAERN NGRLAMVAIM GLMVQDGMFG EPPLSYMSKN GWWGEGVQYF VQ HLNNCQS FSGSFVDNAG VCALPSRQGR TA

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Macromolecule #3: PCP-11

MacromoleculeName: PCP-11 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 21.707047 KDa
SequenceString: ATKLSEGPFI ETETYPAPKE MEMSAAVPFL RYPQVLKGWV GEEKGFDPLG VTDALPVYWV REAELKHGRV CMLATVGWIA TDLGMRFPG DQFQSVQTTL EAHDKMVEAG LMAPFLGAVG TFELYSLWLF FKGWEMEVNR DAGDFFLGKQ FLPKEPAKEK D MRLKELEN ...String:
ATKLSEGPFI ETETYPAPKE MEMSAAVPFL RYPQVLKGWV GEEKGFDPLG VTDALPVYWV REAELKHGRV CMLATVGWIA TDLGMRFPG DQFQSVQTTL EAHDKMVEAG LMAPFLGAVG TFELYSLWLF FKGWEMEVNR DAGDFFLGKQ FLPKEPAKEK D MRLKELEN GRLAMFAFSG IVTQAAMTGQ AWPFM

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Macromolecule #4: PCPI-6

MacromoleculeName: PCPI-6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 19.572627 KDa
SequenceString:
GGYKMSPAVP FLPMSPALEG IPGEEEGFDP MGFSLAIDIR WLREAELKHG RVAMLATVGW IATDLGLRVP GEPFQVSTVE AHDAMVKFG SMPQMLVWMG YAELFGFLAI VNMFEGKTDR KPGDFGLRGF YPQDAKGQYD MQVKELRNGR LAMLAYGGIV T TAVLTQEK WPFFDAVVN

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Macromolecule #5: PCPI-5

MacromoleculeName: PCPI-5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 26.752762 KDa
SequenceString: MAVAAGLLAL PAFVPSSLTG AQAPAAPALR GNSQGSAGAG SASVGIAGAA CAVLGAAALR RGVAARKALR RELAIAYEDS GIDLLDNGK FCQGLAGADG AWGRYEFDPL GFSKKTELVP YFREAELKHG RLAMLAWVGM VVPDFVRIPG EKFSFEAVPL P IDGHDAFS ...String:
MAVAAGLLAL PAFVPSSLTG AQAPAAPALR GNSQGSAGAG SASVGIAGAA CAVLGAAALR RGVAARKALR RELAIAYEDS GIDLLDNGK FCQGLAGADG AWGRYEFDPL GFSKKTELVP YFREAELKHG RLAMLAWVGM VVPDFVRIPG EKFSFEAVPL P IDGHDAFS GATGVNAQIL FWVGILEFCC AKKVFEWNSL EVAGDYGLTK FFPSDEEGQK KMRTAELKNG RLAMLAFGGA IT QAVITRH PFPWLY

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Macromolecule #6: PCPI-8

MacromoleculeName: PCPI-8 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 30.544203 KDa
SequenceString: MEVAFLTPIA TNVASSVAPA HAGKAPGPPG PAGASFGLTA AFGVAAALGL ASRKRVQRAA QEMATLPKHM QPVDTADYPV YKPGPSGVP KLPQLVGDWG VPLPGSYKAC LTMVGPDVET ACEVGKPWDP LGLSKLYDRN FDFNGNMTYP HVQWLRESEL K HGRCAMLA ...String:
MEVAFLTPIA TNVASSVAPA HAGKAPGPPG PAGASFGLTA AFGVAAALGL ASRKRVQRAA QEMATLPKHM QPVDTADYPV YKPGPSGVP KLPQLVGDWG VPLPGSYKAC LTMVGPDVET ACEVGKPWDP LGLSKLYDRN FDFNGNMTYP HVQWLRESEL K HGRCAMLA IVGIFAQQSF HIDGYPEAPW YEALKACYDN PAGIVGFGIA QISAFAMVIE GAYFPKDSWI GQMDREPGDL GF DPLKLAK DAESMKSMQL KELKNGRLAM MAFMSCVVGH YVPGSVPGV

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Macromolecule #7: PCPI-4

MacromoleculeName: PCPI-4 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 24.445182 KDa
SequenceString: MLGLAGAGAV TAASMGVSQR QRVVRRAEFA AGMAGSKLHG WGEYQFDPAG FATSYPELLG WFRESELKHG RVAMLAYVGL IVPDAFRLP FEEVQDSSLD LLSAHNKLIG PGLGEGPMWW LLLACGVIES FRFKQVGLAF ESLTTENAGD LGLRMFAPSS A EGMESMKM ...String:
MLGLAGAGAV TAASMGVSQR QRVVRRAEFA AGMAGSKLHG WGEYQFDPAG FATSYPELLG WFRESELKHG RVAMLAYVGL IVPDAFRLP FEEVQDSSLD LLSAHNKLIG PGLGEGPMWW LLLACGVIES FRFKQVGLAF ESLTTENAGD LGLRMFAPSS A EGMESMKM KELKNGRLAM LAIGGALTQG VLFNAHHFPF MSALRSEKQS GIGSRSTMVG TAASMGVSQR

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Macromolecule #8: PCPI-10

MacromoleculeName: PCPI-10 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 27.998846 KDa
SequenceString: MALGAAAAAY LGSSAVQAFL APSAPSPALR GAPGTSGTSA SASSSGFSAT SFGATAVATA ALALARRGRG LVPRAAEAEP FAGGLIGGE SAFAGQDFNF DPLGLATKCE KFLPWFREAE LKHGRIAMLA WVGLVAPEFV RIPGPEQCYG AKTVVEAHNA C AGDPYFPF ...String:
MALGAAAAAY LGSSAVQAFL APSAPSPALR GAPGTSGTSA SASSSGFSAT SFGATAVATA ALALARRGRG LVPRAAEAEP FAGGLIGGE SAFAGQDFNF DPLGLATKCE KFLPWFREAE LKHGRIAMLA WVGLVAPEFV RIPGPEQCYG AKTVVEAHNA C AGDPYFPF IIDATDFYGK DGHQVGPLFQ VFAFCGAVEM LTTFAKTANV SNKPGLTLAN AGDYRLGANF LPEDEAKAKE MK LKELKNG RLAMLAFGGA ITQATLTGNG FPWL

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Macromolecule #9: PCPI-3

MacromoleculeName: PCPI-3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 27.409289 KDa
SequenceString: MFFQDGLTGS AWGDWALYTD SPLRALTPAQ ESIAGTGGPF PENFWDPAGI TSKKSKEEIL ELRAIELKHG RVAMLAVLGW FHVAAGFHI IGDLATGTYL DNNPLVSVTQ LPMGGMWQTV FFIMCLEWVS TYVCPPPKSK PWDILGWSDI LLEDEDNYWN Q FRKAEVQE ...String:
MFFQDGLTGS AWGDWALYTD SPLRALTPAQ ESIAGTGGPF PENFWDPAGI TSKKSKEEIL ELRAIELKHG RVAMLAVLGW FHVAAGFHI IGDLATGTYL DNNPLVSVTQ LPMGGMWQTV FFIMCLEWVS TYVCPPPKSK PWDILGWSDI LLEDEDNYWN Q FRKAEVQE LNNGRLAMMA IVGLIVQDIF FGDFGEVKVC FSSQTCQDIG DYLPGWTGPL PPVAYDFPPL YPAPEVPYTG YQ APLKLM

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Macromolecule #10: PCPI-9

MacromoleculeName: PCPI-9 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 22.091139 KDa
SequenceString: MAIIGMFFQD GLTGSAWGDW ANYTDSPLRA FEGELGVQAP VGYFDPLGLS KDGDVETFRR RRESELKNGR VAMFATIGYM VPEYFKFPG YLAPSASLKF ADVPNGIQAI TKVPAEGWLQ WVALCGCYEL CVNQPVDAAD PGNYGKGKLG YGNMVLGITA E SISDPEAR ...String:
MAIIGMFFQD GLTGSAWGDW ANYTDSPLRA FEGELGVQAP VGYFDPLGLS KDGDVETFRR RRESELKNGR VAMFATIGYM VPEYFKFPG YLAPSASLKF ADVPNGIQAI TKVPAEGWLQ WVALCGCYEL CVNQPVDAAD PGNYGKGKLG YGNMVLGITA E SISDPEAR KRGLNSELAN GRLAMMAIMG LWVQDGLFGT PYGLY

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Macromolecule #11: PCPI-13

MacromoleculeName: PCPI-13 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 23.286387 KDa
SequenceString: MLAIAGCGLS YQAFVQTAGS SHGAPTQALR GNASQATRTN LSSASVSAAA SITGLAVLGA SRARGDKVRR CAEFNGADMP GATAPLGWF DPLGLGKTEE RFNKMRAAEL KHGRVAMMAS LGCVVQHWAK FPGFESAPAG LGALSNPAAL GGMGALFLGC G VLELGFWS ...String:
MLAIAGCGLS YQAFVQTAGS SHGAPTQALR GNASQATRTN LSSASVSAAA SITGLAVLGA SRARGDKVRR CAEFNGADMP GATAPLGWF DPLGLGKTEE RFNKMRAAEL KHGRVAMMAS LGCVVQHWAK FPGFESAPAG LGALSNPAAL GGMGALFLGC G VLELGFWS DEAAKEPGNF GDPANFSAEY GAYSKEFRDK EINHGRMAMM AIIGQLSAEA VTGMDAAQ

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Macromolecule #12: PCPI-12

MacromoleculeName: PCPI-12 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 21.881955 KDa
SequenceString: MAIIGQLSAE AVTGMDAAQQ AGLAAVARPR QIQSSSAFVG AASIAPKRLT ARRAFDASQE AGVTAPLGYF DPAGFVQDEE SFLNLRRAE IKHGRVAMMA ALGLLVQSLI KLPGFDSVPA GLGAQWTAPG DAGLWTVVVL CGFFETGLNQ WREDPKQPGN F GDPMNLGN ...String:
MAIIGQLSAE AVTGMDAAQQ AGLAAVARPR QIQSSSAFVG AASIAPKRLT ARRAFDASQE AGVTAPLGYF DPAGFVQDEE SFLNLRRAE IKHGRVAMMA ALGLLVQSLI KLPGFDSVPA GLGAQWTAPG DAGLWTVVVL CGFFETGLNQ WREDPKQPGN F GDPMNLGN YTMEMRNKEL NNGRIAMFAV MGIISAEIYT GNVAVAQF

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Macromolecule #13: PCPI-2

MacromoleculeName: PCPI-2 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 15.403753 KDa
SequenceString:
SETFRRRRIS EIKNGRVAMI ACMGYIAPEY FRWPGYCSPS TDLKFADIPN GIQALYKMPA EAWAQIGVFI AFLELFPMRQ EKDALPGDA PNFGRLGVPF FSSKADPEKN RRGLEAEINN GRLAMVAITG MISQNAFF

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Macromolecule #14: PsaA

MacromoleculeName: PsaA / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 76.579406 KDa
SequenceString: AIFRYVNATL WSKAGHFNKA LSKGAKTTTW IWNLHASAHD FDIQQGSAGL IARKVFSSGL AHLSLVFFWL GGMHFHGAYL SNYSAWLKD PKSVAPSSHI AYSLVGQDIL NSYTSQYFSG ITITSGFFQL YRSEGIVTQS QLKYACAASL IATLICLSGS Y LHMQLMSK ...String:
AIFRYVNATL WSKAGHFNKA LSKGAKTTTW IWNLHASAHD FDIQQGSAGL IARKVFSSGL AHLSLVFFWL GGMHFHGAYL SNYSAWLKD PKSVAPSSHI AYSLVGQDIL NSYTSQYFSG ITITSGFFQL YRSEGIVTQS QLKYACAASL IATLICLSGS Y LHMQLMSK FTSFYKKFQS LSQSHLIIMF GFGSVSFSAH QIHEALPINS LLDSGIWDPQ LFSAITGKST MAILLGTPSA IT GKLLNPS TGSIFLSQVA AHHLAVGIVF ITLGLIKWCN LFFSRNAILS LRLAYMDYHA QLSINLAVWA SLSMVAAHHL TEI PVYPYE STDYPTVLCL FVHHACLSGF FTVASGAHAS IFVIRQLPTS EIRHRDPIIG HLIWVCIALG LHSFGLYCHN DTLE ALGRP EDTFCDNSIQ LKPIFAKQFL GLQPGIEVLD GKIVRMTQEL GTADFMVHHI HAFTIHVTLL ILLKGVLYAR NSRLV SDKL ELGFAYPCDG PGRGGTCQIS PWDHLFLAVF WMYNCLSVVI FHYFWKMQSD VWGSYVHLSQ HLQLHCCSSL AHSSLT CSH YSQGDFSVNS ITINGWLRNL LWSEASQVIQ SYALPSICSY GFIFLAAHFV WAFSLMFLFS GRAYWQELIE SILWSHH KL KIVPHIQPRA LSISQGRAVG LTHYVLGGIG CTWAFIISRM LVLTT

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Macromolecule #15: PsaB

MacromoleculeName: PsaB / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 74.857719 KDa
SequenceString: MSFNGRCATS RYLQVMGSIH DIESYFALDN TLSLNLQIFT AHWGHLAIIL MWISGNLYHI ASNANYSLWI KNPIPSMPIA HNIWDPHFT SSTSTPYSHT TTAAVLIAYS GIYNQLYTSG FSTVNQIYKA TFAFSCLAVI SILLAKIHIR THSEVLHNSA T HASQIPSF ...String:
MSFNGRCATS RYLQVMGSIH DIESYFALDN TLSLNLQIFT AHWGHLAIIL MWISGNLYHI ASNANYSLWI KNPIPSMPIA HNIWDPHFT SSTSTPYSHT TTAAVLIAYS GIYNQLYTSG FSTVNQIYKA TFAFSCLAVI SILLAKIHIR THSEVLHNSA T HASQIPSF FQLLYFLDVG ISSINIRLNF HTGVLVGFFS IAYTGHLLDV AIPASRAPLS HTSLSYLTFF GGLKSDTASL YL TDIAHHH LAIGVIFVYI GHLYSSCSTA LGTYIRDMLY TSAIYMFQIK SLHLALSLAL AGCAVLTSAT AQHIYSLTPY FYL SYDYVT SVTLYVHHSY IASFLAIASH AHAAITLVRD WVAPLELESS CTIARIHTHK AAIISHLSWV SLWLGFHTLA IYSH NDTNM AFGSPSKQIL IEPTNAQLIQ ESSGKALYSF AINSLANYNK SFGSFIYPIG PGDLYVHHAI ALGLHVTVLI LLKGA LEAR GSKLMPDKME HSFGFSCDGP GRGGTCDISA WDCFYLAMFW MLNTNAWIDF YFHYKYLAPR QFSESSTYLE SWFRDY LWF NSAPLIRAYS ALGTNDLSVQ AWFFLLTHLA WATGFMFLIS WRGYWQELID IILYMHLKTP ILIDLWNGGV YTPLALS IV QARFIGLVHF TAGLILTYPP FIISTTS

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Macromolecule #16: PsaC

MacromoleculeName: PsaC / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 16.733236 KDa
SequenceString:
MSRLLMIAAC AGLAARYVPQ AFVPGLAQGA APSTPHASFA EGKSTGALAG FAAVSCAIGA GAAAVQSRAA RMARRSHAVK IYDTCIGCT LCVRACPTDV LEMVPATVNA AKQVASSPRV EDCVGCKRCE TACPTDFLSI RVYLQENEET QYSLGLDLAD W S

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Macromolecule #17: PsaD

MacromoleculeName: PsaD / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 32.748867 KDa
SequenceString: MASRGVGVAA VAVFGLATVA FVAPSSGARR LRAPVAQPAA FGASAPSGTS GLWTACSLGG VVLAVGAAVT RRAESKEIVV ESIPRPEDL LESPKFPMFE GSTGGYMSRS TRERHAITWT AKDQNKFEMP TGGFAIMNKG ENLCYFRKKE QCISLGKQLR K MKIENYKI ...String:
MASRGVGVAA VAVFGLATVA FVAPSSGARR LRAPVAQPAA FGASAPSGTS GLWTACSLGG VVLAVGAAVT RRAESKEIVV ESIPRPEDL LESPKFPMFE GSTGGYMSRS TRERHAITWT AKDQNKFEMP TGGFAIMNKG ENLCYFRKKE QCISLGKQLR K MKIENYKI YRLKKDGTVI FMHPADGVFP EKVNKGRVQV NGRPFTIRGN PQQSELKWTK YHMKSYEADP LTTLFIKARV MA FQDIPNL FALPQPNMEE MVPVEEVGEY TKQEYTTRLM EALKRVQDDR KAKEAKSL

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Macromolecule #18: PsaE

MacromoleculeName: PsaE / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 13.089105 KDa
SequenceString:
MARVRSLALL LAAAYALAPC FVGSAAALDG SRLGATARSA EAKKKAKAPW VGPKKGSWVK VLRPESYWYQ TRGQVVNVNQ KPEIKYPVT VKFDRVNFSN VNTNGFALWE VIEAPAPGPG EV

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Macromolecule #19: PsaF

MacromoleculeName: PsaF / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 29.733779 KDa
SequenceString: MARPGSALLC VAAATVLVAA AVAFVGSPAG THAPSTGRSV ELGSRALPPA AESAAASGEA AAEQSGAESF MKWTAAGLLA GLVMAVSSS TPASALPKPT DMFGGVDIDL ENTPEHWTIK ASKRLELCKD NKAYKKKFKD ELYKTEKQQK KYATGSAVYA R FNKKIAQI ...String:
MARPGSALLC VAAATVLVAA AVAFVGSPAG THAPSTGRSV ELGSRALPPA AESAAASGEA AAEQSGAESF MKWTAAGLLA GLVMAVSSS TPASALPKPT DMFGGVDIDL ENTPEHWTIK ASKRLELCKD NKAYKKKFKD ELYKTEKQQK KYATGSAVYA R FNKKIAQI KNRQEAYGDR LCGKQDGNPR VVATGEWNVR ASVMWPASIF LYTAGWIGWA GRSYLIRTND ETKELNIDVP LA LTCMASG FSWPVAAWQE IVNGEMAVPS SQIHPGGPYT QS

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Macromolecule #20: PsaI

MacromoleculeName: PsaI / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 19.725674 KDa
SequenceString:
MARPGRMLLV ALAAVLGLSY CFLSSPEKLP KAKGVDFNAA VAASAALPAL TMLAEDAEAK YGDNRKWSAV LVPLTTLVFP AVAMGSFVL YSFQEDAFWR LVPGTKRAAE AEKAWREHPL FKDSKDPMFG LLNPDDYEKG LEEAWERAKP AGSTVTVKDK L KQLSKQDS PHWESWRSLS A

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Macromolecule #21: PsaJ

MacromoleculeName: PsaJ / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 15.832114 KDa
SequenceString:
MARFTNLILV AACVLLGNRF YTLLFANAPS QNLRSHVAVR AVDERDEGLV LITPEESGKV VKRDVNNNPP RIVMKTNDWD QPEIQLSTG ASNQINYITP VVASDDIKAW LSLNVNFFSI LALLTVGGII EIQRFFPDTL YW

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Macromolecule #22: PsaL

MacromoleculeName: PsaL / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 38.708449 KDa
SequenceString: MRDFASVSTA LTLAAVCACT VLLTGDVLAF TAGVSRGPQL PPHATGASSL AGSSMPFASA QEVMGAKGVV CFGMGFGVLL ALSRGLSQS RVSCKAEGSD IAVKEKADIS KIAYLQDVPR TILEADVLEK LLMNTPRDQW EDPPEDTYLY TLKTFAEVYG P GKATKMGW ...String:
MRDFASVSTA LTLAAVCACT VLLTGDVLAF TAGVSRGPQL PPHATGASSL AGSSMPFASA QEVMGAKGVV CFGMGFGVLL ALSRGLSQS RVSCKAEGSD IAVKEKADIS KIAYLQDVPR TILEADVLEK LLMNTPRDQW EDPPEDTYLY TLKTFAEVYG P GKATKMGW WDYFRLKLDL PPGFELLDED EMKVAADYDK LMMEGKIPFA VPGPAGFWYT GAVIQWKGKE QFAGDQVQTL TE NGRFSKQ FLANLAFYRD GLKPWQRGLE IGMAHGYFLI GPFTSLGPLR NTPEAATVGL LCGCAIVGLV SIGGLIFGST IKP TRFDKE GDKPASGFIE MINWHAIGGL GGAGFAHALI TVFGS

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Macromolecule #23: PsaM

MacromoleculeName: PsaM / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 14.96978 KDa
SequenceString:
MARSPLILCL VAAAVMLVAP RAFVSSPKSQ NAAALTAGVA AGSMVMPAWA YDQQMMDAQL LLARVPGGKR TKELGLVVPI PEEDGLTDG QIAALFVVAL VVLIAAVDLA RSLYFGLQPN KFKTAKGKGS ITPFMKRLIE NGF

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Macromolecule #24: PsaR

MacromoleculeName: PsaR / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 17.253617 KDa
SequenceString:
MGLAAAWRAR SSTAAGAEGG AYKETPADER LFEQVYLQYT SEYMKGPMYW HKDKLQGSLP DYPGRPMIRD GKYTPYVLGN LKSFSSNEL AFLSMLFFGV GLYGNLQFNY YDPQWAKVDA GGYFNVSYIV ESLLLPISFF MHIACYIQKQ NGK

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Macromolecule #25: PsaT

MacromoleculeName: PsaT / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 13.40001 KDa
SequenceString:
MSRRAGSVVV LGALACLVWG PSFTGSVPRR QESALARMAS SKWVNPEDPE MSHPSGLYVL PLKPAKPQEN YIYTWKKGED GSIEDYVKT PFKGPERAAD YYTQRKGNGA WDHWGPQGEG EA

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Macromolecule #26: PsaU

MacromoleculeName: PsaU / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Molecular weightTheoretical: 24.303311 KDa
SequenceString: MARSLAVAAL IAVAGGLAFV PGAIPRGTTA PPSRALQAAP AAESSWGSLP TLVGGMALGV FFSLATLAPV RAEEAPATPA PTPAEQAPT PAPGPSDEEI LAKGCDIRVD CTTKEQQFAW AKAYYRKYNQ ETDGKDPKYS KPSTGAGVFR KFKIDWPNPD P SIPDTTDG ...String:
MARSLAVAAL IAVAGGLAFV PGAIPRGTTA PPSRALQAAP AAESSWGSLP TLVGGMALGV FFSLATLAPV RAEEAPATPA PTPAEQAPT PAPGPSDEEI LAKGCDIRVD CTTKEQQFAW AKAYYRKYNQ ETDGKDPKYS KPSTGAGVFR KFKIDWPNPD P SIPDTTDG TYPIRNEDFL PIWKQQQEDL RAKMKEYIGR EFTEIRWIGD YDNARSPYKP HNGYY

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Macromolecule #27: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 27 / Number of copies: 196 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #28: Chlorophyll c2

MacromoleculeName: Chlorophyll c2 / type: ligand / ID: 28 / Number of copies: 20 / Formula: KC2
Molecular weightTheoretical: 608.926 Da
Chemical component information

ChemComp-KC2:
Chlorophyll c2

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Macromolecule #29: [(1~{S},5~{R})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9...

MacromoleculeName: [(1~{S},5~{R})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0] ...Name: [(1~{S},5~{R})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl] ethanoate
type: ligand / ID: 29 / Number of copies: 16 / Formula: UIX
Molecular weightTheoretical: 642.907 Da

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Macromolecule #30: (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: 30 / Number of copies: 41 / 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 #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: 3 / 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: PERIDININ

MacromoleculeName: PERIDININ / type: ligand / ID: 32 / Number of copies: 10 / Formula: PID
Molecular weightTheoretical: 630.81 Da
Chemical component information

ChemComp-PID:
PERIDININ

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Macromolecule #33: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 33 / Number of copies: 7 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #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

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Macromolecule #35: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 35 / Number of copies: 4 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #36: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 36 / Number of copies: 1 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #37: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 37 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #38: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 38 / Number of copies: 13 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #39: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 39 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 161863
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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