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- EMDB-63405: PSI-4 LHCI dimer supercomplex from M. polymorpha -

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Basic information

Entry
Database: EMDB / ID: EMD-63405
TitlePSI-4 LHCI dimer supercomplex from M. polymorpha
Map data
Sample
  • Complex: Photosystem I-4 LHCI dimer supercomplex from liverwort
    • Protein or peptide: x 17 types
  • Ligand: x 12 types
KeywordsPhotosystem I / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / response to low light intensity stimulus / plastid thylakoid membrane / thylakoid membrane / response to high light intensity / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosystem I reaction center ...photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / response to low light intensity stimulus / plastid thylakoid membrane / thylakoid membrane / response to high light intensity / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / response to cold / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein stabilization / protein domain specific binding / mRNA binding / magnesium ion binding / metal ion binding
Similarity search - Function
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 PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I psaG and psaK proteins signature. ...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 PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 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 reaction center subunit II, chloroplastic / PSI-K / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit III / Uncharacterized protein / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit VI, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A1 ...Photosystem I reaction center subunit II, chloroplastic / PSI-K / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit III / Uncharacterized protein / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit VI, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A1 / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesMarchantia polymorpha (common liverwort)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsTsai P-C / La Rocca R / Shen J-R / Akita F
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22H04916 Japan
CitationJournal: Commun Biol / Year: 2026
Title: Structural study of monomeric and dimeric photosystem I-LHCI supercomplexes from a bryophyte.
Authors: Pi-Cheng Tsai / Romain La Rocca / Hiroyasu Motose / Jian-Ren Shen / Fusamichi Akita /
Abstract: Photosystem I (PSI) is one of the two photosystems conserved from cyanobacteria to vascular plants, and associates with multiple light-harvesting complexes (LHCs) that capture and transfer solar ...Photosystem I (PSI) is one of the two photosystems conserved from cyanobacteria to vascular plants, and associates with multiple light-harvesting complexes (LHCs) that capture and transfer solar energy. Liverworts such as Marchantia polymorpha occupy an early evolutionary position among land plants and faced major challenges during terrestrial adaptation, including desiccation, strong light, and UV radiation. We reveal the cryo-electron microscopic structures of PSI-LHCI monomer and homodimer from the liverwort M. polymorpha at resolutions of 1.94 and 2.52 Å, respectively. The high-resolution map allows identification of the cofactors of the monomer and reveal differences between the liverwort and moss, another clade of bryophytes. The PSI-LHCI monomer-monomer is stabilized by PsaG and PsaH interactions on the stromal side, which causes the bending and twisting of the homodimer. PsaM interacts with PsaB tightly, indicating a key role of PsaM in mediating the dimerization.
History
DepositionFeb 10, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63405.png

Downloads & links

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Map

FileDownload / File: emd_63405.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 640 pix.
= 465.28 Å		0.73 Å/pix.
x 640 pix.
= 465.28 Å		0.73 Å/pix.
x 640 pix.
= 465.28 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.08748231 - 0.23182137
Average (Standard dev.)-0.00005252088 (±0.0062412624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 465.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63405_msk_1.map
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Additional map: #1

Fileemd_63405_additional_1.map
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Half map: #2

Fileemd_63405_half_map_1.map
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Half map: #1

Fileemd_63405_half_map_2.map
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Sample components

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Entire : Photosystem I-4 LHCI dimer supercomplex from liverwort

EntireName: Photosystem I-4 LHCI dimer supercomplex from liverwort
Components
  • Complex: Photosystem I-4 LHCI dimer supercomplex from liverwort
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: Photosystem I reaction center subunit II, chloroplastic
    • Protein or peptide: Photosystem I reaction centre subunit IV
    • 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: PSI subunit V
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • 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, chloroplastic
    • Protein or peptide: PSI-K
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: BETA-CAROTENE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: EICOSANE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: CHLOROPHYLL B

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Supramolecule #1: Photosystem I-4 LHCI dimer supercomplex from liverwort

SupramoleculeName: Photosystem I-4 LHCI dimer supercomplex from liverwort
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Marchantia polymorpha (common liverwort)

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Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Molecular weightTheoretical: 82.484688 KDa
SequenceString: MASRFPKFSQ GLSQDPTTRR IWFGIATAHD FESHDDMTEE RLYQKIFASH FGQLAIIFLW TSGNLFHVAW QGNFEAWGQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA SGPVNIAYSG VYQWWYTIGL RTNQDLYNGA LFLVILSSIS LIAGWLHLQP K WKPKVSWF ...String:
MASRFPKFSQ GLSQDPTTRR IWFGIATAHD FESHDDMTEE RLYQKIFASH FGQLAIIFLW TSGNLFHVAW QGNFEAWGQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA SGPVNIAYSG VYQWWYTIGL RTNQDLYNGA LFLVILSSIS LIAGWLHLQP K WKPKVSWF KNAESRLNHH LSGLFGVSSL AWTGHLVHVA IPESRGEHVR WDNFLTKLPH PEGLGPFFAG QWNVYAQNVD SS NHAFGTS QGAGTAILTF IGGFHPQTQS LWLTDIAHHH LAIAVVFIIA GHMYRTNFGI GHSIKEILET HTPPGGRLGR GHK GLYDTI NNSLHFQLGL ALASLGVITS LVAQHMYSLP PYAFLAQDFT TQAALYTHHQ YIAGFIMTGA FAHGAIFFIR DYNP EQNKD NVLARMLEHK EAIISHLSWA SLFLGFHTLG LYVHNDVMLA FGTPEKQILI EPIFAQWIQS AHGKALYGFD VLLSS TNNP AFNAGQSIWL PGWLDAINNN SNSLFLTIGP GDFLVHHAIA LGLHTTTLIL VKGALDARGS KLMPDKKEFG YSFPCD GPG RGGTCDISAW DAFYLAVFWM LNTIGWVTFY WHWKHITLWQ GNAAQFNESS TYLMGWLRDY LWLNSSQLIN GYNPFGM NS LSVWAWMFLF GHLVWATGFM FLISWRGYWQ ELIETLAWAH ERTPLANLVR WKDKPVALSI VQARLVGLAH FSVGYIFT Y AAFLIASTSG KFG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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Macromolecule #2: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Molecular weightTheoretical: 8.866216 KDa
SequenceString:
MAHAVKIYDT CIGCTQCVRA CPTDVLEMIP WDGCKANQIA SAPRTEDCVG CKRCESACPT DFLSVRVYLG DETTRSMGLS Y

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #3: Photosystem I reaction center subunit II, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit II, chloroplastic
type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Molecular weightTheoretical: 22.614096 KDa
SequenceString: MASLACTSAV AAVAATGPVA KIENGSTNVA RSLAMAPLKA SSLHGQKMSV ASSAARVTMA AAGKAPAAEA PAGFTPPELK ADTPSPIFG GSTGGLLRKA QVEEFYVITW DSPKEQIFEM PTGGAAIMRS GPNLLKLARK EQCLALGTAL RTKFKIKYQF Y RVFPNGEV ...String:
MASLACTSAV AAVAATGPVA KIENGSTNVA RSLAMAPLKA SSLHGQKMSV ASSAARVTMA AAGKAPAAEA PAGFTPPELK ADTPSPIFG GSTGGLLRKA QVEEFYVITW DSPKEQIFEM PTGGAAIMRS GPNLLKLARK EQCLALGTAL RTKFKIKYQF Y RVFPNGEV QYLHPKDGVY PEKVNAGRTA VGFNSRSIGK NKNPAEIKFG KAPAFEL

UniProtKB: Photosystem I reaction center subunit II, chloroplastic

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Macromolecule #4: Photosystem I reaction centre subunit IV

MacromoleculeName: Photosystem I reaction centre subunit IV / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Molecular weightTheoretical: 13.821722 KDa
SequenceString:
MAAAASSMLA MVAAPAAGLS SNVSQTRVQI RRVGAARFPR FTIRAADAPA EPAAAAPAAA PEKAAPPPPF GPKRGSTVKI MRPESYWFN ETGTVVSVDQ TPGLRYPVVV RFTKCNYAGV NTNNYGIDEV SSV

UniProtKB: Uncharacterized protein

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Macromolecule #5: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Molecular weightTheoretical: 26.025164 KDa
SequenceString: MATVSMAAIS PAGLVAPLNV SSKSTFAAST KVSAFVKNVR ARTVCSASAE KEQTVGETAG KIATALALAA VVGTASFVAP EDAMADVAG LTPCKESKAF AKREKNEIKA LEKRLKLYGA DSAPALAIKA TVEKTKRRFA FYGNEGLLCG TDGLPHLIVD G DQAHLGEF ...String:
MATVSMAAIS PAGLVAPLNV SSKSTFAAST KVSAFVKNVR ARTVCSASAE KEQTVGETAG KIATALALAA VVGTASFVAP EDAMADVAG LTPCKESKAF AKREKNEIKA LEKRLKLYGA DSAPALAIKA TVEKTKRRFA FYGNEGLLCG TDGLPHLIVD G DQAHLGEF VYPGVVFLYI AGWIGWVGRS YLIAIRGEKK PTEKEIIIDV PLATSLLWKG LTWPVAALSE LRTGKLIEDA SN ITVSPR

UniProtKB: Photosystem I reaction center subunit III

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Macromolecule #6: Photosystem I reaction center subunit V, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit V, chloroplastic
type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Molecular weightTheoretical: 16.912248 KDa
SequenceString:
MASCTAQIAV AAGVPALAAR SKSIRASSSQ VSFSGRNMVS CVSISNRSWE SQTKLARANA RTVCADTSLV ISLSTGALLF LGRFVLLPF QRKQVSQAGL PRQNGVTHFE AGDARAQEVS SLMKTNDPAG FTIVDLLAWG ALGHAVGFFI LATASNGYDP T F

UniProtKB: Photosystem I reaction center subunit V, chloroplastic

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Macromolecule #7: Photosystem I reaction center subunit VI, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit VI, chloroplastic
type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Molecular weightTheoretical: 14.660665 KDa
SequenceString:
MASIVAVAGP SVVAGLGSSS LSGQKLRVST RSFSVRAAPS VGVASAKYDA GNSKYFDLED LGNTTGAWDL YGSDQLSPYN GMQSKFFET FAYPLTKRGI LLKLGLLGGA LALGFASSSA TGDILAIKKG PQGPPQMGPR NRI

UniProtKB: Photosystem I reaction center subunit VI, chloroplastic

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Macromolecule #8: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Molecular weightTheoretical: 4.017787 KDa
SequenceString:
MTASYLPSIF VPLVGLIFPA ITMASLFIYI EQDEIL

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #9: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Molecular weightTheoretical: 4.77865 KDa
SequenceString:
MQDVKTYLST APVLATLWFG FLAGLLIEIN RFFPDALVLP FF

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #10: PSI subunit V

MacromoleculeName: PSI subunit V / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Molecular weightTheoretical: 23.152729 KDa
SequenceString: MATAAMVRAG GLLSLQQTAT KNVVRSSFVG SAAPLRFRSA SSSVSVRPMS IRAGATTEGK YQVVEPLNGD PFVGGLETPV TSSPLIAWY LSNLPAYRTA VSPLLRGVEV GLAHGFLLVG PFVKTGPLRN TDIAGPAGSF AAAGLVVILS VCLTMYGIAQ F KEGAASIA ...String:
MATAAMVRAG GLLSLQQTAT KNVVRSSFVG SAAPLRFRSA SSSVSVRPMS IRAGATTEGK YQVVEPLNGD PFVGGLETPV TSSPLIAWY LSNLPAYRTA VSPLLRGVEV GLAHGFLLVG PFVKTGPLRN TDIAGPAGSF AAAGLVVILS VCLTMYGIAQ F KEGAASIA PSLTLSGRKK EADKLQTAQG WASFSGGFFF GGLSGVYWAY FLLYVVNLPY FVK

UniProtKB: Photosystem I reaction center subunit XI, chloroplastic

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Macromolecule #11: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Molecular weightTheoretical: 3.568273 KDa
SequenceString:
MTSISDSQII VILLSVFITS ILALRLGKEL YQ

UniProtKB: Photosystem I reaction center subunit XII

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Macromolecule #12: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Molecular weightTheoretical: 83.299375 KDa
SequenceString: MTIRSPEPEV KIVVEKDPVK TSFEKWAKPG HFSRTLAKGP STTTWIWNLH ADAHDFDSHT NDLEEISRKV FSAHFGQLAI IFIWLSGMY FHGARFSNYE AWLSDPTHIK PSAQVVWPIV GQEILNGDVG GGFQGIQITS GFFQLWRASG ITSELQLYST A IGGLVFAA ...String:
MTIRSPEPEV KIVVEKDPVK TSFEKWAKPG HFSRTLAKGP STTTWIWNLH ADAHDFDSHT NDLEEISRKV FSAHFGQLAI IFIWLSGMY FHGARFSNYE AWLSDPTHIK PSAQVVWPIV GQEILNGDVG GGFQGIQITS GFFQLWRASG ITSELQLYST A IGGLVFAA LMLFAGWFHY HKAAPKLAWF QDVESMLNHH LAGLLGLGSL SWAGHQVHVS LPINQLLDAG VDPKEIPLPH EF ILNRDLL AELYPSFAKG LTPFFTLNWS EYSDFLTFRG GLNPVTGGLW LTDTAHHHLA IAVLFLVAGH MYRTNWGIGH SFK EILEAH KGPFTGEGHK GLYEILTTSW HAQLALNLAM LGSLTIIVAH HMYAMPPYPY LATDYGTQLS LFTHHMWIGG FLIV GAAAH AAIFMVRDYD PTTQYNNLLD RVLRHRDAII SHLNWVCIFL GFHSFGLYIH NDTMSALGRP QDMFSDTAIQ LQPVF AQWI QNTHALAPNF TAPNALASTS LTWGGGDVIA VGSKVALLPI PLGTADFLVH HIHAFTIHVT VLILLKGVLF ARSSRL IPD KANLGFRFPC DGPGRGGTCQ VSAWDHVFLG LFWMYNSISV VIFHFSWKMQ SDVWGTISEE GVVTHITGGN FAQSAIT IN GWLRDFLWAQ ASQVIQSYGS SLSAYGLLFL GAHFVWAFSL MFLFSGRGYW QELIESIVWA HNKLKVAPAI QPRALSIT Q GRAVGVAHYL LGGIATTWAF FLARIIAVG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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Macromolecule #13: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Molecular weightTheoretical: 28.576648 KDa
SequenceString: MATAVCTTSR IASIAPSTSA TKAVSSGSAV KAAFFGKTLR SAKVSAVSKA SFSVRAQATE RPLWFPGSTA PEWLDGSLPG DFGFDPLGL GSEPELLKWF VQAEIVHCRW AMLGAAGIFI PELLTKIGIL NTPSWYTAGE QTYFADQTTL FIVELLFMGW A EGRRWADI ...String:
MATAVCTTSR IASIAPSTSA TKAVSSGSAV KAAFFGKTLR SAKVSAVSKA SFSVRAQATE RPLWFPGSTA PEWLDGSLPG DFGFDPLGL GSEPELLKWF VQAEIVHCRW AMLGAAGIFI PELLTKIGIL NTPSWYTAGE QTYFADQTTL FIVELLFMGW A EGRRWADI LKPGSVNTDP VFPNNKLTGT DVGYPGGFWF DPLGWGAGGA AKVKELRTKE IKNGRLAMLA VMGAWFQAVY TG TGPIDNL FAHLADPGHA TVFAALDKLQ

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #14: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Molecular weightTheoretical: 30.133443 KDa
SequenceString: MATTVACRAV AGAVFAPAQE QRLMGGNALR VSFAPIGTSN ARSSIVVRAS SDKPVKANRQ LIFASEQSLS YLDGSLPGDY GFDPLGLSD PQGAGGFIDP NWLRYAEIIN GRFAMLGAAG AIAPEIFGKI GLIPQETAIP WFQTGVIPPL GQYSYWADPY T LFVLEMAL ...String:
MATTVACRAV AGAVFAPAQE QRLMGGNALR VSFAPIGTSN ARSSIVVRAS SDKPVKANRQ LIFASEQSLS YLDGSLPGDY GFDPLGLSD PQGAGGFIDP NWLRYAEIIN GRFAMLGAAG AIAPEIFGKI GLIPQETAIP WFQTGVIPPL GQYSYWADPY T LFVLEMAL MGFAEHRRAQ DYYKPGSMGK QYFLGFEKVL GGSGDPAYPG GPLFNFLGFG RDEKSMKDLK VKEVKNGRLA ML AVLGYFI QAIFTGVGPF QNLLDHLSDP ANNNVLTNLK IH

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #15: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Molecular weightTheoretical: 27.114066 KDa
SequenceString: MASVSMQAMS VSSAVCKTSF LSGTSSTRFS RNVQVAAAPI SSQSLKVEAK KGEWLPGLPS PAYLNGSLAG DNGFDPLGLA EDPAALNWY VQAELQNGRW AMLGVAGMLV PEVLTKIGLI NAPLWYDAGK VEYFAPASTL FVIEFILFHY VEIRRWQDIK Y PGSVSQDP ...String:
MASVSMQAMS VSSAVCKTSF LSGTSSTRFS RNVQVAAAPI SSQSLKVEAK KGEWLPGLPS PAYLNGSLAG DNGFDPLGLA EDPAALNWY VQAELQNGRW AMLGVAGMLV PEVLTKIGLI NAPLWYDAGK VEYFAPASTL FVIEFILFHY VEIRRWQDIK Y PGSVSQDP FFKSYKLPPG DVGYPGGIFN PLKFPANQEY KEKEIANGRL AMLAFLGMLV QSKLTGAGPF ENLLTHLADP WH TTIVQTL AN

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #16: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Molecular weightTheoretical: 26.038801 KDa
SequenceString: MAAATMACVG LSAPALLSGA QRTKFFSGHV SSLSTVSNGS RVSMSSEWMP GQPRPAYLDG SSPGDFGFDP LGLAEVPENF ARYKESELI HCRWAMLAVP GVLIPEALGL GNWVSAQQWA ATPGGQATYL GNPVPWGTLP IILAIEFLAV AFVEAKRGEE P DHEKRKYP ...String:
MAAATMACVG LSAPALLSGA QRTKFFSGHV SSLSTVSNGS RVSMSSEWMP GQPRPAYLDG SSPGDFGFDP LGLAEVPENF ARYKESELI HCRWAMLAVP GVLIPEALGL GNWVSAQQWA ATPGGQATYL GNPVPWGTLP IILAIEFLAV AFVEAKRGEE P DHEKRKYP GGPFDPLGFA KDPKKLEEYK LKELKNGRLA LLAFLGFSVQ AIAYPGTGPL ENLASHLSNP WANNIANIII PR SVL

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #17: PSI-K

MacromoleculeName: PSI-K / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Molecular weightTheoretical: 13.483683 KDa
SequenceString:
MATSIVSASA VVAAPAREFA GLRATTSFGK VQNVAMLPKS VNGKGALGAR CDYIGSSTNL IMVASTTLML FAGRFGLAPS ANRKALSGL KLVDRDSGLQ TGDPAGFTAT DTLACGVMGH IIGVGIVLGL KATGGL

UniProtKB: PSI-K

+
Macromolecule #18: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 18 / Number of copies: 276 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #19: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 19 / Number of copies: 4 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

+
Macromolecule #20: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 20 / Number of copies: 42 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #21: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 21 / Number of copies: 2 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #22: EICOSANE

MacromoleculeName: EICOSANE / type: ligand / ID: 22 / Number of copies: 4 / Formula: LFA
Molecular weightTheoretical: 282.547 Da
Chemical component information

ChemComp-LFA:
EICOSANE

+
Macromolecule #23: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 23 / Number of copies: 10 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #24: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 24 / Number of copies: 6 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #25: (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: 25 / Number of copies: 20 / 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

+
Macromolecule #26: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 26 / Number of copies: 2 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 27 / Number of copies: 12 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #28: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 28 / Number of copies: 6 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

+
Macromolecule #29: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 29 / Number of copies: 28 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.007 kPa / Details: 10 mA
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
Details1.46 mg Chl a per mL

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: TFS Selectris X
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 17907 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2164638
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Initial model generated from the data
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 27750
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9luu:
PSI-4 LHCI dimer supercomplex from M. polymorpha

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