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- EMDB-66932: In situ structure of the PSI-LHCI-LHCII supercomplex from Oryza sativa -

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Basic information

Entry
Database: EMDB / ID: EMD-66932
TitleIn situ structure of the PSI-LHCI-LHCII supercomplex from Oryza sativa
Map data
Sample
  • Complex: In situ structure of the PSI-LHCI-LHCII supercomplex from Oryza sativa
    • Protein or peptide: x 2 types
  • Protein or peptide: x 18 types
  • Ligand: x 11 types
KeywordsPhotosystem I / PSI-LHCI-LHCII / in situ / Oryza sativa / PHOTOSYNTHESIS
Function / homology
Function and homology information


chloroplast photosystem I / photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / plastid ...chloroplast photosystem I / photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / plastid / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein domain specific binding / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily ...Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / 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 / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / 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 reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaA / Photosystem I protein PsaC / 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
Chlorophyll A-B binding protein / Photosystem I reaction center subunit N, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Chlorophyll a-b binding protein 1, chloroplastic / : / Photosystem I reaction center subunit VI, chloroplastic ...Chlorophyll A-B binding protein / Photosystem I reaction center subunit N, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Chlorophyll a-b binding protein 1, chloroplastic / : / Photosystem I reaction center subunit VI, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit IV / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit II, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit III / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice) / Oryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsLi J / Elias E / Zhang K / Croce R / Zhu J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2026
Title: In situ structures of plant photosystem supercomplexes.
Authors: Jiao Li / Eduard Elias / Kai Zhang / Roberta Croce / Jiapeng Zhu /
Abstract: Photosynthesis sustains life on Earth by converting light to chemical energy through the coordinated action of photosystem I (PSI) and photosystem II (PSII) within thylakoid membranes. Although ...Photosynthesis sustains life on Earth by converting light to chemical energy through the coordinated action of photosystem I (PSI) and photosystem II (PSII) within thylakoid membranes. Although structures of isolated photosystems are available, their native organization in chloroplasts remains unknown. Here, using in situ cryo-electron microscopy, we directly imaged Oryza sativa (rice) chloroplasts and determined structures of photosystem supercomplexes in their native membrane environment. We resolved a CSML-type PSII-light harvesting complex II (LHCII) supercomplex, including four LHCII antenna trimers that were not retained in purified preparations. Excitation energy transfer calculations based on this architecture closely reproduce in vivo measurements, indicating its physiological relevance. We also resolved asymmetric PSII-LHCII dimers, including side-by-side, trans-lumenal and trans-stromal architectures, and higher-order assemblies of trimers and tetramers. On the basis of these observations, we propose that PSII forms a trans-lumenal and trans-stromal 'skeleton' that shapes thylakoid morphology and supports grana stacking. In addition, we obtained high-resolution structures of PSI-LHCI-LHCII and PSI-LHCI supercomplexes. Together, these structures reveal extensive networks of lipids, pigments and cofactors, providing the first molecular framework for understanding how the native architecture of plant photosystem supports the exceptional photon-to-electron efficiency of photosynthesis.
History
DepositionNov 4, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66932.png

Downloads & links

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Map

FileDownload / File: emd_66932.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.19135 - 0.62199324
Average (Standard dev.)0.00019385865 (±0.012116994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66932_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_66932_half_map_2.map
Projections & Slices
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Sample components

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Entire : In situ structure of the PSI-LHCI-LHCII supercomplex from Oryza sativa

EntireName: In situ structure of the PSI-LHCI-LHCII supercomplex from Oryza sativa
Components
  • Complex: In situ structure of the PSI-LHCI-LHCII supercomplex from Oryza sativa
    • Protein or peptide: Photosystem I reaction center subunit II, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit IV
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Protein or peptide: Chlorophyll A-B binding protein
  • 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 III
  • Protein or peptide: Photosystem I reaction center subunit V, chloroplastic
  • Protein or peptide: Photosystem I reaction center subunit VI, chloroplastic
  • 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 psaK, chloroplastic
  • Protein or peptide: Photosystem I reaction center subunit XI, chloroplastic
  • Protein or peptide: Photosystem I reaction center subunit N, chloroplastic
  • Protein or peptide: H0622F05.3 protein
  • Protein or peptide: Chlorophyll a-b binding protein 1, chloroplastic
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • 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: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Supramolecule #1: In situ structure of the PSI-LHCI-LHCII supercomplex from Oryza sativa

SupramoleculeName: In situ structure of the PSI-LHCI-LHCII supercomplex from Oryza sativa
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #8-#9
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)

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Macromolecule #1: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 22.068029 KDa
SequenceString: SAEWMPGQPR PAHLDGSSPG DFGFDPLGLA TVPENFERFK ESEVYHCRWA MLAVPGVLVP EALGLGNWVQ AQEWAAEPGG QATYLGNPV PWGTLPTILV IEFVAIAFAE HQRTMEKDPE KKKYPGGAFD PLGFSKDPVK FEEYKLKEIK NGRLAMLAFV G FCVQQSAY ...String:
SAEWMPGQPR PAHLDGSSPG DFGFDPLGLA TVPENFERFK ESEVYHCRWA MLAVPGVLVP EALGLGNWVQ AQEWAAEPGG QATYLGNPV PWGTLPTILV IEFVAIAFAE HQRTMEKDPE KKKYPGGAFD PLGFSKDPVK FEEYKLKEIK NGRLAMLAFV G FCVQQSAY PGTGPLENLA SHLSDPWHNN IGDIIIPRTI YP

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #2: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 22.765832 KDa
SequenceString: AAPDRPIWFP GSTPPPWLDG SLPGDFGFDP LGLGSDPESL RWNVQAELVH CRWAMLGAAG IFIPEFLTKI GILNTPSWYT AGEQQYFTD TTTLFIIELI LIGWAEGRRW ADIIKPGCVN TDPIFPNNKL TGTDVGYPGG LWFDPLGWGT GSPEKIKELR T KEIKNGRL ...String:
AAPDRPIWFP GSTPPPWLDG SLPGDFGFDP LGLGSDPESL RWNVQAELVH CRWAMLGAAG IFIPEFLTKI GILNTPSWYT AGEQQYFTD TTTLFIIELI LIGWAEGRRW ADIIKPGCVN TDPIFPNNKL TGTDVGYPGG LWFDPLGWGT GSPEKIKELR T KEIKNGRL AMLAVMGAWF QAEYTGTGPI DNLFAHLADP GHATIFQAF

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #3: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 24.33585 KDa
SequenceString: RQLWFASKQS LSYLDGTLPG DFGFDPLGLS DPEGTGGFIE PRWLAYGEVF NGRTAMMGVV GMVAPELLGK LGLVPAETAI PWFQTGVIP PAGTYTYWAD PYTLFVFELA LVGFAEHRRF QDWYTPGSMG KQYFLGLEKY LAGSGEPAYP GGPLFNPLGF G TKSEAEMK ...String:
RQLWFASKQS LSYLDGTLPG DFGFDPLGLS DPEGTGGFIE PRWLAYGEVF NGRTAMMGVV GMVAPELLGK LGLVPAETAI PWFQTGVIP PAGTYTYWAD PYTLFVFELA LVGFAEHRRF QDWYTPGSMG KQYFLGLEKY LAGSGEPAYP GGPLFNPLGF G TKSEAEMK ELKLKEIKNG RLAMLAFLGF SVQALFTGVG PVQNLLDHLA DPVHNNILTS LKFH

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #4: Chlorophyll A-B binding protein

MacromoleculeName: Chlorophyll A-B binding protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 22.188219 KDa
SequenceString: KGEWLPGLPS PTYLNGSLPG DNGFDPLGLA EDPENLRWFV QAELVNGRWA MLGVAGMLLP EVLTKIGLID APQWYDAGKA TYFASSSTL FVIEFILFHY VEIRRWQDIK NPGCVNQDPI FKSYSLPPHE CGYPGSVFNP LNFEPTLEAK EKELANGRLA M LAFLGFLV ...String:
KGEWLPGLPS PTYLNGSLPG DNGFDPLGLA EDPENLRWFV QAELVNGRWA MLGVAGMLLP EVLTKIGLID APQWYDAGKA TYFASSSTL FVIEFILFHY VEIRRWQDIK NPGCVNQDPI FKSYSLPPHE CGYPGSVFNP LNFEPTLEAK EKELANGRLA M LAFLGFLV QHNVTQKGPF DNLLQHLSDP WHNTIIQTLS

UniProtKB: Chlorophyll A-B binding protein

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Macromolecule #5: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 82.310055 KDa
SequenceString: EVKIVVDRDP VKTSFEEWAR PGHFSRTIAK GPDTTTWIWN LHADAHDFDS HTGDLEEISR KVFSAHFGQL SIIFLWLSGM YFHGARFSN YEAWLSDPTH IGPSAQVVWP IVGQEILNGD VGGGFRGIQI TSGFFQIWRA SGITSELQLY CTAIGALIFA S LMLFAGWF ...String:
EVKIVVDRDP VKTSFEEWAR PGHFSRTIAK GPDTTTWIWN LHADAHDFDS HTGDLEEISR KVFSAHFGQL SIIFLWLSGM YFHGARFSN YEAWLSDPTH IGPSAQVVWP IVGQEILNGD VGGGFRGIQI TSGFFQIWRA SGITSELQLY CTAIGALIFA S LMLFAGWF HYHKAAPKLA WFQDVESMLN HHLAGLLGLG SLSWAGHQIH VSLPINQFLD AGVDPKEIPL PHEFILNRDL LA QLYPSFA EGATPFFTLN WSKYAEFLSF RGGLDPITGG LWLSDIAHHH LAIAILFLIA GHMYRTNWGI GHGLKDILEA HKG PFTGQG HKGLYEILTT SWHAQLSLNL AMLGSTTIVV AHHMYSMPPY PYLATDYGTQ LSLFTHHMWI GGFLIVGAAA HAAI FMVRD YDPTTRYNDL LDRVLRHRDA IISHLNWVCI FLGFHSFGLY IHNDTMSALG RPQDMFSDTA IQLQPIFAQW VQNLH AGAP SVTAPGATTS TSLTWGGGEL VAVGGKVALL PIPLGTADFL VHHIHAFTIH VTVLILLKGV LFARSSRLIP DKANLG FRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNSI SVVIFHFSWK MQSDVWGTIS DQGVVTHITG GNFAQSSITI NGWLRDF LW AQASQVIQSY GSSLSAYGLF FLGAHFVWAF SLMFLFSGRG YWQELIESIV WAHNKLKVAP ATQPRALSII QGRAVGVT H YLLGGIATTW AFFLARIIAV G

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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Macromolecule #6: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 82.3785 KDa
SequenceString: LRFPRFSQGL AQDPTTRRIW FGIATAHDFE SHDDITEERL YQNIFASHFG QLAIIFLWTS GNLFHVAWQG NFESWIQDPL HVRPIAHAI WDPHFGQPAV EAFTRGGAAG PVNIAYSGVY QWWYTIGLRT NEDLYTGALF LLFLSTLSLI GGWLHLQPKW K PSLSWFKN ...String:
LRFPRFSQGL AQDPTTRRIW FGIATAHDFE SHDDITEERL YQNIFASHFG QLAIIFLWTS GNLFHVAWQG NFESWIQDPL HVRPIAHAI WDPHFGQPAV EAFTRGGAAG PVNIAYSGVY QWWYTIGLRT NEDLYTGALF LLFLSTLSLI GGWLHLQPKW K PSLSWFKN AESRLNHHLS GLFGVSSLAW TGHLVHVAIP ASRGEYVRWN NFLDVLPYPQ GLGPLLTGQW NLYAQNPDSS NH LFGTTQG AGTAILTLLG GFHPQTQSLW LTDIAHHHLA IAFIFLIAGH MYRTNFGIGH SIKDLLEAHT PPGGRLGRGH KGL YDTINN SIHFQLGLAL ASLGVITSLV AQHMYSLPSY AFIAQDFTTQ AALYTHHQYI AGFIMTGAFA HGAIFFIRDY NPEQ NEDNV LARMLDHKEA IISHLSWASL FLGFHTLGLY VHNDVMLAFG TPEKQILIEP IFAQWIQSAH GKTTYGFDIL LSSTS GPAF NAGRTLWLPG WLNAVNENSN SLFLTIGPGD FLVHHAIALG LHTTTLILVK GALDARGSKL MPDKKDFGYS FPCDGP GRG GTCDISAWDA FYLAVFWMLN TIGWVTFYWH WKHITLWQGN VSQFNESSTY LMGWLRDYLW LNSSQLINGY NPFGMNS LS VWAWMFLFGH LVWATGFMFL ISWRGYWQEL IETLAWAHER TPLANLIRWR DKPVALSIVQ ARLVGLAHFS VGYIFTYA A FLIASTSGKF G

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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Macromolecule #7: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 8.778149 KDa
SequenceString:
SHSVKIYDTC IGCTQCVRAC PTDVLEMIPW DGCKAKQIAS APRTEDCVGC KRCESACPTD FLSVRVYLGP ETTRSMALSY

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #8: Photosystem I reaction center subunit II, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit II, chloroplastic
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 15.983311 KDa
SequenceString:
GFVPPQLDPN TPSPIFGGST GGLLRKAQVE EFYVITWTSP KEQVFEMPTG GAAIMREGPN LLKLARKEQC LALGTRLRSK YKINYQFYR VFPNGEVQYL HPKDGVYPEK VNAGRQGVGQ NFRSIGKNVS PIEVKFTGKN VFDI

UniProtKB: Photosystem I reaction center subunit II, chloroplastic

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Macromolecule #9: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 7.466427 KDa
SequenceString:
PPIGPKRGTK VKILRRESYW YNGTGSVVTV DQDPNTRYPV VVRFAKVNYA GVSTNNYALD EIQEVK

UniProtKB: Photosystem I reaction center subunit IV

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Macromolecule #10: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 17.514418 KDa
SequenceString:
DIAGLTPCKE SKAFAKREKQ SIKKLQSSLK KYAPDSAPAL AINATIEKTK RRFENYGKFG LLCGADGLPH LIVSGDQRHW GEFITPGLL FLYIAGWIGW VGRSYLIAIS GEKKPAMREI IIDVELAVKL LPRGFIWPVA AYRELITGNL VVDDADIGY

UniProtKB: Photosystem I reaction center subunit III

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Macromolecule #11: Photosystem I reaction center subunit V, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit V, chloroplastic
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 10.711042 KDa
SequenceString:
LSPSLVISLS TGVSLFLGRF VFFNFQRENV AKQVPEQNGK THFDAGDERA KEFAGLLRSN DPVGFNLVDV LAWGSLGHIV AYYILATCS NGYNPNFF

UniProtKB: Photosystem I reaction center subunit V, chloroplastic

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Macromolecule #12: Photosystem I reaction center subunit VI, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit VI, chloroplastic
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 10.002326 KDa
SequenceString:
YGEKSVYFDL EDIGNTTGQW DLYGSDAPSP YNPLQSKFFE TFAGPFTKRG LLLKFLLLGG GSLVAYVSAS ASPDLLPIKK GPQLPPTPG PRGK

UniProtKB: Photosystem I reaction center subunit VI, chloroplastic

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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: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 3.293013 KDa
SequenceString:
NLPSIFVPLV GLVFPAIAMA SLFLYVQKNK

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: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 4.981871 KDa
SequenceString:
MRDIKTYLSV APVLSTLWFG ALAGLLIEIN RLFPDALSFP FFSF

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #15: Photosystem I reaction center subunit psaK, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit psaK, chloroplastic
type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 8.884315 KDa
SequenceString:
YIGSATNVIM VTTTTLMLFA GRFGLAPSAN RKSTAGLKLE ARDSGLQTGD PAGFTLADTL ACGAVGHIMG VGVVLGLKNI GVLDQIIG

UniProtKB: Photosystem I reaction center subunit psaK, chloroplastic

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Macromolecule #16: Photosystem I reaction center subunit XI, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit XI, chloroplastic
type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 17.252824 KDa
SequenceString:
PTYQVVQPIN GDPFIGSLET PVTSSPLVAW YLSNLPAYRT AVSPLLRGIE VGLAHGYLLV GPFALTGPLR NTPVHGQAGA LGAAGLVAI LSVCLTMYGV ASFGEGEPST APTLTLTGRK KEADKLQTAD GWAKFTGGFF FGGISGVLWA YFLLYVLDLP Y FFK

UniProtKB: Photosystem I reaction center subunit XI, chloroplastic

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Macromolecule #17: Photosystem I reaction center subunit N, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit N, chloroplastic
type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 9.746997 KDa
SequenceString:
VFDEYLEKSK ANKELNDKKR LATSGANFAR AYTVEFGSCQ FPYNFTGCQD LAKQKKVPFI SDDLEIECEG KEKYKCGSNV FWKW

UniProtKB: Photosystem I reaction center subunit N, chloroplastic

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Macromolecule #18: H0622F05.3 protein

MacromoleculeName: H0622F05.3 protein / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 10.276702 KDa
SequenceString:
TFPQDWLRRD LNVIGFGLIG WIAPSSVPAI NGNSLTGLFF SSIGQELSHF PSPPALDSPF WLWLVTWHLG LFLALTFGQI GFKGRTEGY FDK

UniProtKB: UNIPROTKB: Q01L93

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Macromolecule #19: Chlorophyll a-b binding protein 1, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 1, chloroplastic / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 23.368408 KDa
SequenceString: SPWYGADRVL YLGPLSGEPP SYLTGEFPGD YGWDTAGLSA DPETFAKNRE LEVIHSRWAM LGALGCVFPE LLARNGVKFG EAVWFKAGS QIFSEGGLDY LGNPSLIHAQ SILAIWAVQV VLMGAVEGYR IAGGPLGEVV DPLYPGGAFD PLGLADDPEA F AELKVKEI ...String:
SPWYGADRVL YLGPLSGEPP SYLTGEFPGD YGWDTAGLSA DPETFAKNRE LEVIHSRWAM LGALGCVFPE LLARNGVKFG EAVWFKAGS QIFSEGGLDY LGNPSLIHAQ SILAIWAVQV VLMGAVEGYR IAGGPLGEVV DPLYPGGAFD PLGLADDPEA F AELKVKEI KNGRLAMFSM FGFFVQAIVT GKGPLENLAD HLADPVNNNA WAYATNFVPG

UniProtKB: Chlorophyll a-b binding protein 1, chloroplastic

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Macromolecule #20: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 24.04515 KDa
SequenceString: APQSIWYGPD RPKYLGPFSE QTPSYLTGEF PGDYGWDTAG LSADPETFAR NRELEVIHSR WAMLGALGCV FPEILSKNGV KFGEAVWFK AGAQIFSEGG LDYLGNPNLV HAQSILAIWA VQVVLMGFVE GYRVGGGPLG EGLDKVYPGG AFDPLGLADD P DTFAELKV ...String:
APQSIWYGPD RPKYLGPFSE QTPSYLTGEF PGDYGWDTAG LSADPETFAR NRELEVIHSR WAMLGALGCV FPEILSKNGV KFGEAVWFK AGAQIFSEGG LDYLGNPNLV HAQSILAIWA VQVVLMGFVE GYRVGGGPLG EGLDKVYPGG AFDPLGLADD P DTFAELKV KELKNGRLAM FSMFGFFVQA IVTGKGPIEN LFDHVADPVA NNAWAYATNF VPGK

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #21: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 21 / Number of copies: 30 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Macromolecule #22: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 22 / Number of copies: 177 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #23: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

MacromoleculeName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 23 / Number of copies: 5 / Formula: LUT
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-LUT:
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Macromolecule #24: (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: 24 / Number of copies: 4 / 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 #25: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 25 / Number of copies: 30 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #26: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 26 / Number of copies: 24 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #27: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL...

MacromoleculeName: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
type: ligand / ID: 27 / Number of copies: 6 / Formula: MGE
Molecular weightTheoretical: 688.972 Da
Chemical component information

ChemComp-MGE:
(1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE

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Macromolecule #28: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 28 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #29: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 29 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #30: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 30 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #31: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 31 / Number of copies: 4 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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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: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.375 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.4000000000000001 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: PDB ENTRY
PDB model - PDB ID:

5zji

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 124514
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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