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- EMDB-60293: Structure of the astaxanthin mutant PSI-7VCPI supercomplex in Nan... -

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Basic information

Entry
Database: EMDB / ID: EMD-60293
TitleStructure of the astaxanthin mutant PSI-7VCPI supercomplex in Nannochloropsis oceanica
Map data
Sample
  • Complex: Ast-PSI-7VCPI
    • Protein or peptide: x 18 types
  • Ligand: x 11 types
KeywordsPSI-VCPI supercomplex / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III ...Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / : / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit II / Photosystem I reaction center subunit III / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / PSI subunit V
Similarity search - Component
Biological speciesNannochloropsis oceanica strain IMET1 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsShen LL / Shen JR / Wang WD
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Structure of the astaxanthin mutant PSI-7VCPI supercomplex in Nannochloropsis oceanica
Authors: Shen LL / Shen JR / Wang WD
History
DepositionMay 28, 2024-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60293.png

Downloads & links

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Map

FileDownload / File: emd_60293.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.39581585 - 1.55776
Average (Standard dev.)0.0000449856 (±0.024825957)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #2

Fileemd_60293_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60293_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ast-PSI-7VCPI

EntireName: Ast-PSI-7VCPI
Components
  • Complex: Ast-PSI-7VCPI
    • Protein or peptide: VCPI-5
    • Protein or peptide: VCPI-9
    • Protein or peptide: VCPI-8
    • Protein or peptide: VCPI-4/7
    • Protein or peptide: VCPI-6
    • Protein or peptide: VCPI-1
    • 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 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: PsaR
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: PSI subunit V
    • Protein or peptide: PsaM
    • Protein or peptide: PsaS
    • Protein or peptide: Photosystem I iron-sulfur center
  • Ligand: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: (1~{R},3~{S})-6-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{Z},17~{E})-16-(hydroxymethyl)-3,7,12-trimethyl-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]-1,5,5-trimethyl-cyclohexane-1,3-diol
  • Ligand: CHLOROPHYLL A
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: [(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-17-[(4~{S},6~{R})-4-acetyloxy-2,2,6-trimethyl-6-oxidanyl-cyclohexylidene]-6,11,15-trimethyl-2-[(~{E})-2-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]ethenyl]heptadeca-2,4,6,8,10,12,14,16-octaenyl] octanoate
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: PHYLLOQUINONE
  • Ligand: BETA-CAROTENE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Supramolecule #1: Ast-PSI-7VCPI

SupramoleculeName: Ast-PSI-7VCPI / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)

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Macromolecule #1: VCPI-5

MacromoleculeName: VCPI-5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 25.849219 KDa
SequenceString: MFRKLALALL CSSAVAFQVP APLTRGSVRL HAEGKPAAPP AAAPPAAAPA AAAPAAAAPA AAAVKPPPPP PPPKVFSKSV PFLLKPAGL DGMVGDVGFD PLGFATFIDI RWLREAELKN GRVAMLAFLG FIVQEFIRLP GDLYSEPNGV KAFFQVGPQP L LQIFLFCG ...String:
MFRKLALALL CSSAVAFQVP APLTRGSVRL HAEGKPAAPP AAAPPAAAPA AAAPAAAAPA AAAVKPPPPP PPPKVFSKSV PFLLKPAGL DGMVGDVGFD PLGFATFIDI RWLREAELKN GRVAMLAFLG FIVQEFIRLP GDLYSEPNGV KAFFQVGPQP L LQIFLFCG FLEFNMHKGK LTQVDMFEDG KREPGNFGFD PLGFGKDPAK RERYALAELK NGRLAMIAIG GLVHHALVTG HA TFSS

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Macromolecule #2: VCPI-9

MacromoleculeName: VCPI-9 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 24.17598 KDa
SequenceString: MKTAAILAVL ACAANAFVFP TPKVSQTVVR GTPFDTVSKD ELAVENKAMA GKSVFERAMA DFNGRYPAVA ALGLGPSAKA ERWNGRHAM FGWIVLLATG YAQAHGLLPE GGMDAKEWGT WVIVSTTNGE QVTIPAARAA IAIGHLHFGA VGVFAAYSKN S VKDRLLLE ...String:
MKTAAILAVL ACAANAFVFP TPKVSQTVVR GTPFDTVSKD ELAVENKAMA GKSVFERAMA DFNGRYPAVA ALGLGPSAKA ERWNGRHAM FGWIVLLATG YAQAHGLLPE GGMDAKEWGT WVIVSTTNGE QVTIPAARAA IAIGHLHFGA VGVFAAYSKN S VKDRLLLE PGEKDEAPAG LFPALRPGLT KEAEMLNGRV AMLGLVALVA VSAATGQDIL SVIDQGLGGL LLKA

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Macromolecule #3: VCPI-8

MacromoleculeName: VCPI-8 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 21.633426 KDa
SequenceString: MKVTAVLSLL AAPLLASAFI APAPKATRAR GVMSMAQSKA LPFLKAPAKL DGSLAGDFGF DPMGISDQVA NLKYVRAAEL KHCRVAMLG FLGWVVQQYV HLPGEIYAES NPLKALTSVP LLSQIQIFLF IGAIELATLD QTYTADKPWD LGFDPLNFSK G KSEQQMKD ...String:
MKVTAVLSLL AAPLLASAFI APAPKATRAR GVMSMAQSKA LPFLKAPAKL DGSLAGDFGF DPMGISDQVA NLKYVRAAEL KHCRVAMLG FLGWVVQQYV HLPGEIYAES NPLKALTSVP LLSQIQIFLF IGAIELATLD QTYTADKPWD LGFDPLNFSK G KSEQQMKD LEVKELKNGR VAMIAIMGLI AQTLYTGVPL FS

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Macromolecule #4: VCPI-4/7

MacromoleculeName: VCPI-4/7 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 21.611303 KDa
SequenceString: MKLLSFACLL GAATAFVPSM PTTTRTRGAV RMMAEKSKAV PFLPRPAALD GSVVGDVGFD PVGFTSWLPL SYLQEAEIKH CRIAMLATL GWIVADFVHL PGAVHEVSSL AAHDVAVKSG ALAQILIWTS IAEAISVIAI SQMLEGSGRQ PGDFKFDPLN F AKDEKSLK ...String:
MKLLSFACLL GAATAFVPSM PTTTRTRGAV RMMAEKSKAV PFLPRPAALD GSVVGDVGFD PVGFTSWLPL SYLQEAEIKH CRIAMLATL GWIVADFVHL PGAVHEVSSL AAHDVAVKSG ALAQILIWTS IAEAISVIAI SQMLEGSGRQ PGDFKFDPLN F AKDEKSLK KMQLSELKNG RLAMLAFSGI VTQAALTGHA FPYM

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Macromolecule #5: VCPI-6

MacromoleculeName: VCPI-6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 27.655738 KDa
SequenceString: MHHDARPTAR RTAVGTQTSS ASSCRHPSAH SPHPTTTSQH RSSFRNMKCI VFAGLLASAT AFIAPAPRAS SRSVMKMGLE NQVGFDIET GGKPWDPFGF AGVSERNGLG ILPHIKWLQE SEIKHGRTAM LAFLGVIVPG SLGIYVPTYP QEPDFTKAFS A ALQSNPLG ...String:
MHHDARPTAR RTAVGTQTSS ASSCRHPSAH SPHPTTTSQH RSSFRNMKCI VFAGLLASAT AFIAPAPRAS SRSVMKMGLE NQVGFDIET GGKPWDPFGF AGVSERNGLG ILPHIKWLQE SEIKHGRTAM LAFLGVIVPG SLGIYVPTYP QEPDFTKAFS A ALQSNPLG MAQIALAVAI IEGHYYAGDF WTGGGDRQVG AFGFDPLGFS KGKSEAAIKS MQLKEIKNGR LAMIAMAAFA SE KFIPGSV PLLHSAFPTL PI

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Macromolecule #6: VCPI-1

MacromoleculeName: VCPI-1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 22.652133 KDa
SequenceString: MVGIHKTLLV AAVTMASVSA FVPPAPAAPR TRGVMKMGLD GMIGSSAPFK NFDPLGFAAK ADQKTLNKYR ESELKHGRVA MLAVLGWIV QEFWHPLYDG KLSSNPLKAL TEVPLIGWAQ IFVAINVIEY LQNKIKELPG YRPGDYLGTW EWVEQSDEGW D SYQTKELN ...String:
MVGIHKTLLV AAVTMASVSA FVPPAPAAPR TRGVMKMGLD GMIGSSAPFK NFDPLGFAAK ADQKTLNKYR ESELKHGRVA MLAVLGWIV QEFWHPLYDG KLSSNPLKAL TEVPLIGWAQ IFVAINVIEY LQNKIKELPG YRPGDYLGTW EWVEQSDEGW D SYQTKELN NGRLAMVAIA GLIVQDLITG QAALEQITAG NTGVFSGLGK

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Macromolecule #7: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 82.797758 KDa
SequenceString: MSTTRKSTIV DFNPVETSFE KWAKPGQFSR TLAKGPKTTT WIWNLHADAH DFDIQTNSLQ EVSRKIFSAH FGQLAVIFLW LSGMHFHGA YFSNYSAWLT NPTSTKPSAQ IVWPIVGQEV LNADVGGNFQ GIQITSGFFQ LWRAEGITSE VELYWTAVGG L VASFLMLF ...String:
MSTTRKSTIV DFNPVETSFE KWAKPGQFSR TLAKGPKTTT WIWNLHADAH DFDIQTNSLQ EVSRKIFSAH FGQLAVIFLW LSGMHFHGA YFSNYSAWLT NPTSTKPSAQ IVWPIVGQEV LNADVGGNFQ GIQITSGFFQ LWRAEGITSE VELYWTAVGG L VASFLMLF AGWFHYHKAA PKLEWFQNVE SMLNHHLAGL LGLGSLSWAG HQIHIALPIN KLLDLGVSPE EIPLPYEFIL NR DLIAQLY PSFNKGLTPF FTLNWGEYSD FLTFKGGLNP VTGGLWLTDT AHHHLAIAVL FIVAGHMYKT NWFLGHSIKT ILE AHKGPF TGEGHKGLYE VLTTSWHAQL AINLALFGSL SIIVAHHMYA MPPYPYIAID YPTQLSLFTH HVWIGGFCIV GGAA HGAIF FVRDYNAANN YNNLIDRVIR HRDAIISHLN WVCIFLGCHS FGLYVHNDTM RALGRSQDLF SDNAIALKPI FAQFI QNLH TLAPGSTAPN ALTTVSYAFG GDVISVGSKI AMMPISLGTA DFLVHHIHAF TIHVTVLILL KGVLYSRNSR LIPDKA NLG FRFPCDGPGR GGTCQVSAWD HVFLGLFWMY NSISIVIFHF SWKMQSDVWG TVSPTGAVSH ITGGNFAQSS ITINGWL RD FLWSQAAQVV QSYGSSLSAY GLIFLGAHFI WAFSLMFLFS GRGYWQELIE SIVWAHNKLK VAPSIQPRAL SITQGRAV G VAHYLLGGIG TTWAFFLARI ISVG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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Macromolecule #8: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 82.864992 KDa
SequenceString: MVYKFPKFSK ALAEDPSTRR IWYGIATAHD FESHDAMTES KLYQKIFASH FGHIAIIFLW TAGNLFHVAW QGNFEAWILN PLKVRPIAH AIWDPHFGQA AYKAFLKTSS PANLALSGVY EWWYTIGMRT NNDLYQGSFF LILLSSLLLF AGWLHLQPSF R PSLDWFKA ...String:
MVYKFPKFSK ALAEDPSTRR IWYGIATAHD FESHDAMTES KLYQKIFASH FGHIAIIFLW TAGNLFHVAW QGNFEAWILN PLKVRPIAH AIWDPHFGQA AYKAFLKTSS PANLALSGVY EWWYTIGMRT NNDLYQGSFF LILLSSLLLF AGWLHLQPSF R PSLDWFKA NEYRLNHHLS GLFGVSSLAW TGHLVHVAIP ESRGIHVGWD NFLTVLPHPE GLTPFFSGNW KAYAQNPDTA SH IFGSGEG SGTAILTFLG GFHPQTKSLW LTDMAHHHLA IAVLFIVAGH MYRTNWLIGH QMKLILEAHR PPGGRLGIGH IGL YETITN SLHFQLGLAL AALGVATSLT AQHMYALPPY AFLASNFPTQ AALYTHHQYI AGFLMVGAFA HGAIFFVRDY DPAV NTRNG EKNVLARMLE HKEAIISHLS WVSLFLGFHT LGIYVHNDVV VAFGQPEKQI LVEPLFAEWI QAASGKTLYN FDLLL ASSN SPASVASSQL WLPGWLSAIN DGKNSLFLPI GPGDFLVHHA IALGLHTTTL ILVKGALDAR GSKLMPDKKD FGYSFP CDG PGRGGTCDIS AWDAFYLAMF WMLNTIGWVT FYWHWKHLTL WQGNQVQFNE SSNYIMGWLR DYLWLNSSPL INGYNPF GM NSLSVWAWMF LFGHLVWATG FMFLISWRGY WQELIETIVW AHERTPLANL VRWKDKPVAL SIVQARLVGL AHFTIGYV L TYAAFVIAST IGKLGY

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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Macromolecule #9: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 15.037159 KDa
SequenceString:
MNLKLKQSDF PKFEGSTGGW LSAAKNEEKY VIIWTSKDAS LFEMPTGGTA KMNAGNNVAY FARKEQCLAL GSQLRGFKIT NYKIFRIYP PLDITLLHPF DGVFPEKVNQ GRSPVGKRDA SIGGNPNPAS LKFQSNT

UniProtKB: Photosystem I reaction center subunit II

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Macromolecule #10: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 7.668697 KDa
SequenceString:
MIQKGSTVRI LRKESYWYNE SGTVVVVDQS KVRYPVLVRF TKVNYAGTNT NNFGLNEVEE VVTKKSS

UniProtKB: Photosystem I reaction center subunit IV

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Macromolecule #11: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 20.813076 KDa
SequenceString:
MTKIVKFAFL PLLTFLGLPM ISNADIGGLN PCKDSEVFQK RLAKTVKKLE NRLKKYEEGT PPQIAIQQQI TQTKQRFTRY ADSNLLCGN DGLPHLITDG RWSHGSEFLL PSILFLYISG WIGWVGRKYI RTVGQTSNPT EKEIIIDVPL AISIMTSGFL W PFAAWQEF LSGDLIASDE TITTSPK

UniProtKB: Photosystem I reaction center subunit III

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Macromolecule #12: PsaR

MacromoleculeName: PsaR / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 13.958494 KDa
SequenceString:
MKTFCILLAL VALFNFSNAF MPKAPVHTAR PVVARGRTMK MMEESTYWEG KAPPSVVLGP FLSKIPSGVL GPASLVALIV GSYCTHESN IFNTLTVDTI YPAYVLGSFL TPISWGLHVA AWIQKMNKA

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Macromolecule #13: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 5.226195 KDa
SequenceString:
MSLDLLPSFF VPLVGLVLPL FSIIGLFLYI EKENREVFDP TTYKF

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #14: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 4.762584 KDa
SequenceString:
MKDFLKYLST APVLLTAWLT FTAGFVIEIN RFYPDALTFP F

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #15: PSI subunit V

MacromoleculeName: PSI subunit V / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 18.695639 KDa
SequenceString:
MVSFIKPYRQ DPFVGHLATP ITTSAFTRAY LKVLPAYRPG LTPLSRGAEI GFTHGYFLIG PFYTYGPLRS VEFSLTSLAA GLLAAITLL LILTVGLSIY GQVTYDVYDN ALIVKLVRQM VGSERTQDLP QIKGTSELDT VLGWQKFSEG FFSGGLIGSI V AAVGIALY STYL

UniProtKB: PSI subunit V

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Macromolecule #16: PsaM

MacromoleculeName: PsaM / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 3.241863 KDa
SequenceString:
MIYDSQVYIA LVIAVVASVL AIRLGATLYN

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Macromolecule #17: PsaS

MacromoleculeName: PsaS / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 4.698783 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)

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Macromolecule #18: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Molecular weightTheoretical: 8.763116 KDa
SequenceString:
MSHTVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCKAGQIA SAPRTEDCVG CKRCETACPT DFLSVRVYLG GETTRSLGLA Y

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #19: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

MacromoleculeName: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 19 / Number of copies: 27 / Formula: XAT
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-XAT:
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Macromolecule #20: (1~{R},3~{S})-6-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{Z},17...

MacromoleculeName: (1~{R},3~{S})-6-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{Z},17~{E})-16-(hydroxymethyl)-3,7,12-trimethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl] ...Name: (1~{R},3~{S})-6-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{Z},17~{E})-16-(hydroxymethyl)-3,7,12-trimethyl-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]-1,5,5-trimethyl-cyclohexane-1,3-diol
type: ligand / ID: 20 / Number of copies: 5 / Formula: A1L1G
Molecular weightTheoretical: 616.87 Da

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Macromolecule #21: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 21 / Number of copies: 168 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #22: 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: 22 / Number of copies: 2 / 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 #23: [(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-17-[(4~{S},6~{R})...

MacromoleculeName: [(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-17-[(4~{S},6~{R})-4-acetyloxy-2,2,6-trimethyl-6-oxidanyl-cyclohexylidene]-6,11,15-trimethyl-2-[(~{E})-2-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4- ...Name: [(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-17-[(4~{S},6~{R})-4-acetyloxy-2,2,6-trimethyl-6-oxidanyl-cyclohexylidene]-6,11,15-trimethyl-2-[(~{E})-2-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]ethenyl]heptadeca-2,4,6,8,10,12,14,16-octaenyl] octanoate
type: ligand / ID: 23 / Number of copies: 6 / Formula: A1L1F
Molecular weightTheoretical: 785.102 Da

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Macromolecule #24: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 24 / Number of copies: 5 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #25: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 25 / Number of copies: 3 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #26: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 26 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #27: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 27 / Number of copies: 19 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #28: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 28 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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

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

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

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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: 7.5
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: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19451
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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