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- EMDB-31350: Barley photosystem I-LHCI-Lhca6 supercomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-31350
TitleBarley photosystem I-LHCI-Lhca6 supercomplex
Map dataPSI-LHCI-A6 supercomplex
Sample
  • Complex: PSI-LHCI-Lhca6 supercomplex of Barley
    • Protein or peptide: x 15 types
  • Ligand: x 11 types
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding
Similarity search - Function
Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I PsaA ...Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / 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
Similarity search - Domain/homology
Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2
Similarity search - Component
Biological speciesHordeum vulgare subsp. spontaneum (wild barley) / Hordeum vulgare (barley)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsWang WD / Shen L / Tang K / Han GY / Zhang X / Shen JR
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesQYZDY-SSW-SMC003 China
CitationJournal: Nature / Year: 2022
Title: Architecture of the chloroplast PSI-NDH supercomplex in Hordeum vulgare.
Authors: Liangliang Shen / Kailu Tang / Wenda Wang / Chen Wang / Hangjun Wu / Zhiyuan Mao / Shaoya An / Shenghai Chang / Tingyun Kuang / Jian-Ren Shen / Guangye Han / Xing Zhang /
Abstract: The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET). The NDH complex ...The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET). The NDH complex associates with PSI to form the PSI-NDH supercomplex and fulfil its function. Here, we report cryo-electron microscopy structures of a PSI-NDH supercomplex from barley (Hordeum vulgare). The structures reveal that PSI-NDH is composed of two copies of the PSI-light-harvesting complex I (LHCI) subcomplex and one NDH complex. Two monomeric LHCI proteins, Lhca5 and Lhca6, mediate the binding of two PSI complexes to NDH. Ten plant chloroplast-specific NDH subunits are presented and their exact positions as well as their interactions with other subunits in NDH are elucidated. In all, this study provides a structural basis for further investigations on the functions and regulation of PSI-NDH-dependent CET.
History
DepositionMay 25, 2021-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateFeb 9, 2022-
Current statusFeb 9, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ewk
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ewk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31350.png

Downloads & links

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Map

FileDownload / File: emd_31350.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPSI-LHCI-A6 supercomplex
Voxel sizeX=Y=Z: 1.307 Å
Density
Contour LevelBy AUTHOR: 0.43 / Movie #1: 0.5
Minimum - Maximum-1.7327698 - 4.5609584
Average (Standard dev.)-0.0008927759 (±0.074390866)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 575.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3071.3071.307
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z575.080575.080575.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-1.7334.561-0.001

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Supplemental data

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Sample components

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Entire : PSI-LHCI-Lhca6 supercomplex of Barley

EntireName: PSI-LHCI-Lhca6 supercomplex of Barley
Components
  • Complex: PSI-LHCI-Lhca6 supercomplex of Barley
    • 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 D
    • Protein or peptide: Photosystem I reaction center subunit E
    • Protein or peptide: Photosystem I reaction center subunit F
    • Protein or peptide: Photosystem I reaction center subunit H
    • 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 K
    • Protein or peptide: Photosystem I reaction center subunit L
    • Protein or peptide: Chlorophyll a-b binding protein Lhca1
    • Protein or peptide: Chlorophyll a-b binding protein Lhca3
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein Lhca6
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: CHLOROPHYLL B
  • 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

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Supramolecule #1: PSI-LHCI-Lhca6 supercomplex of Barley

SupramoleculeName: PSI-LHCI-Lhca6 supercomplex of Barley / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)

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Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 82.29207 KDa
SequenceString: EVKIVVDRDP VKTSFEEWAR PGHFSRTLAK GPDTTTWIWN LHADAHDFDS HTGDLEEISR KVFSAHFGQL SIIFLWLSGM YFHGARFSN YEAWLSDPTH IGPSAQVVWP IVGQEILNGD VGGGFRGIQI TSGFFQLWRA SGITSELQLY CTAIGALVFA A LMLFAGWF ...String:
EVKIVVDRDP VKTSFEEWAR PGHFSRTLAK GPDTTTWIWN LHADAHDFDS HTGDLEEISR KVFSAHFGQL SIIFLWLSGM YFHGARFSN YEAWLSDPTH IGPSAQVVWP IVGQEILNGD VGGGFRGIQI TSGFFQLWRA SGITSELQLY CTAIGALVFA A LMLFAGWF HYHKAAPKLA WFQDVESMLN HHLAGLLGLG SLSWAGHQIH VSLPINQFLD AGVDPKEIPL PHEFILNRDL LA QLYPSFA EGATPFFTLN WSKYAEFLTF RGGLDPVTGG LWLTDIAHHH LAIAILFLIA GHMYRTNWGI GHGLKDILEA HKG PFTGQG HKGLYEILTT SWHAQLSLNL AMLGSTTIVV AHHMYSMPPY PYLATDYGTQ LSLFTHHMWI GGFLIVGAAA HAAI FMVRD YDPTTRYNDL LDRVLRHRDA IISHLNWVCI FLGFHSFGLY IHNDTMSALG RPQDMFSDTA IQLQPIFAQW VQNIH ATAP GVTAPGATTS TSLTWGGGEL VAVGGKVALL PIPLGTADFL VHHIHAFTIH VTVLILLKGV LFARSSRLIP DKANLG FRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNAI SVVIFHFSWK MQSDVWGTIS DQGVVTHITG GNFAQSSITI NGWLRDF LW AQASQVIQSY GSSLSAYGLF FLGAHFVWAF SLMFLFSGRG YWQELIESIV WAHNKLKVAP ATQPRALSII QGRAVGVT H YLLGGIATTW AFFLARIIAV G

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Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 82.562719 KDa
SequenceString: ELRFPRFSQG LAQDPTTRRI WFGIATAHDF ESHDDITEER LYQNIFASHF GQLAIIFLWT SGNLFHVAWQ GNFESWIQDP LHVRPIAHA IWDPHFGQPA VEAFTRGGAA GPVNIAYSGV YQWWYTIGLR TNEDLYTGAL FLLFLSTLSL IASWLHLQPK W KPSLSWFK ...String:
ELRFPRFSQG LAQDPTTRRI WFGIATAHDF ESHDDITEER LYQNIFASHF GQLAIIFLWT SGNLFHVAWQ GNFESWIQDP LHVRPIAHA IWDPHFGQPA VEAFTRGGAA GPVNIAYSGV YQWWYTIGLR TNEDLYTGAL FLLFLSTLSL IASWLHLQPK W KPSLSWFK NAESRLNHHL SGLFGVSSLA WTGHLVHVAI PASRGEYVRW NNFLDVLPYP QGLGPLLTGQ WNLYAQNPDS SN HLFGTAQ GAGTAILTLL GGFHPQTQSL WLTDMAHHHL AIAFIFLIAG HMYRTNFGIG HSIKDLLEAH TPPGGRLGRG HKG LYDTIN NSIHFQLGLA LASLGVITSL VAQHMYSLPP YAFIAQDFTT QAALYTHHQY IAGFIMTGAF AHGAIFFIRD YNPE QNEDN VLARMLDHKE AIISHLSWAS LFLGFHTLGL YVHNDVMLAF GTPEKQILIE PIFAQWIQSA HGKTTYGFDI LLSST NGPA FNAGRSLWLP GWLNAVNENS NSLFLTIGPG DFLVHHAIAL GLHTTTLILV KGALDARGSK LMPDKKDFGY SFPCDG PGR GGTCDISAWD AFYLAVFWML NTIGWVTFYW HWKHITLWQG NVSQFNESST YLMGWLRDYL WLNSSQLING YNPFGMN SL SVWAWMFLFG HLVWATGFMF LISWRGYWQE LIETLAWAHE RTPLANLIRW RDKPVALSIV QARLVGLAHF SVGYIFTY A AFLIASTSGK FG

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Macromolecule #3: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 8.909345 KDa
SequenceString:
MSHSVKIYDT CIGCTQCVRA CPTDVLEMIP WDGCKAKQIA SAPRTEDCVG CKRCESACPT DFLSVRVYLG PETTRSMALS Y

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Macromolecule #4: Photosystem I reaction center subunit D

MacromoleculeName: Photosystem I reaction center subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 15.801046 KDa
SequenceString:
GFVPPQLDPS TPSPIFGGST GGLLRKAQVE EFYVITWTSP KEQVFEMPTG GAAIMREGPN LLKLARKEQC LALGNRLRSK YKIAYQFYR VFPNGEVQYL HPKDGVYPEK VNAGRQGVGQ NFRSIGKNVS PIEVKFTGKN SFD

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Macromolecule #5: Photosystem I reaction center subunit E

MacromoleculeName: Photosystem I reaction center subunit E / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 7.679707 KDa
SequenceString:
KPPPRGPKRG TKVKILRRES YWYNGTGSVV TVDQDPNTRY PVVVRFAKVN YAGVSTNNYA LDEIKEVA

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Macromolecule #6: Photosystem I reaction center subunit F

MacromoleculeName: Photosystem I reaction center subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 17.488256 KDa
SequenceString:
DIAGLTPCKE SKAFAKREKQ SVKKLNSSLK KYAPDSAPAL AIQATIDKTK RRFENYGKFG LLCGSDGLPH LIVSGDQRHW GEFITPGVL FLYIAGWIGW VGRSYLIAVS GEKKPAMREI IIDVELAARI IPRGFIWPVA AYRELINGDL VVDDADIGY

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Macromolecule #7: Photosystem I reaction center subunit H

MacromoleculeName: Photosystem I reaction center subunit H / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 6.431653 KDa
SequenceString:
LQSKFFNTFA APFTKRGLLL KFLLIGGGSL VAYVSASASP DLLPIKKGPQ LPPTPGPRGK I

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 3.338116 KDa
SequenceString:
NLPSIFVPLV GLVFPAIAMT SLFLYVQKKK

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 4.74762 KDa
SequenceString:
MRDIKTYLSV APVLSTLWFG ALAGLLIEIN RLFPDALSFP FF

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Macromolecule #10: Photosystem I reaction center subunit K

MacromoleculeName: Photosystem I reaction center subunit K / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 8.502845 KDa
SequenceString:
YIGSSTNLIM VTTTTLMLFA GRFGLAPSAN RKATAGLKLE ARESGLQTGD PAGFTLADTL ACGAVGHIMG VGIVLGLKNT GVLD

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Macromolecule #11: Photosystem I reaction center subunit L

MacromoleculeName: Photosystem I reaction center subunit L / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 15.512774 KDa
SequenceString:
SLETPVTSSP LVAWYLSNLP AYRTAVSPLL RGIEVGLAHG YLLVGPFALT GPLRNTPVHG QAGTLGAIGL VSILSVCLTM YGVASFNEG EPSTAPVLTL TGRKKEADKL QTAEGWSQFT GGFFFGGVSG AVWAYFLLYV LDLPYFF

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Macromolecule #12: Chlorophyll a-b binding protein Lhca1

MacromoleculeName: Chlorophyll a-b binding protein Lhca1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 21.278209 KDa
SequenceString: EWFPGQPRPA HLDGSSPGDF GFDPLGLATV PENFERFKES EIYHCRWAML CVPGVLVPEA LGLGNWVKAQ EWAALPDGQA TYLGNPVPW GNLPTILAIE FLAIAFAEQQ RTMEKDPEKK KYPGGAFDPL GFSKDPAKFE ELKLKEIKNG RLAMLAFVGF C VQQSAYPG ...String:
EWFPGQPRPA HLDGSSPGDF GFDPLGLATV PENFERFKES EIYHCRWAML CVPGVLVPEA LGLGNWVKAQ EWAALPDGQA TYLGNPVPW GNLPTILAIE FLAIAFAEQQ RTMEKDPEKK KYPGGAFDPL GFSKDPAKFE ELKLKEIKNG RLAMLAFVGF C VQQSAYPG TGPLENLATH LADPWHNNIG DIVIP

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Macromolecule #13: Chlorophyll a-b binding protein Lhca3

MacromoleculeName: Chlorophyll a-b binding protein Lhca3 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 24.395947 KDa
SequenceString: RQLWFASKQS LTYLDGTLPG DFGFDPLGLS DPEGTGGFIE PRWLAYGEIF NGRTAMMGVV GMIAPEALGK VGLVPPETAI PWFQAGAIP PAGTYQYWAD PYTLFVFEMA LIGFAEHRRL QDWYNPGSMG KQYFLGLEKY LGGSGDPAYP GGPIFNPLGF G TKSEKEMK ...String:
RQLWFASKQS LTYLDGTLPG DFGFDPLGLS DPEGTGGFIE PRWLAYGEIF NGRTAMMGVV GMIAPEALGK VGLVPPETAI PWFQAGAIP PAGTYQYWAD PYTLFVFEMA LIGFAEHRRL QDWYNPGSMG KQYFLGLEKY LGGSGDPAYP GGPIFNPLGF G TKSEKEMK ELKLKEIKNG RLAMLAFLGM SLQAIFTGVG PFQNLLDHLS DPVNNNILTS LKFH

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare (barley)
Molecular weightTheoretical: 21.97685 KDa
SequenceString: KGSWLPGLQS PAYLDGSLAG DNGFDPLALA EDPEDLRWFV QAELVNGRWA MLGVAGMLIP EVLTKAGLLN APEWYDAGKE TYFASSSTL FVIEFILFHY VEIRRWQDIK NPGSVNQDPI FKSYSLPPHE CGYPGSVFNP LNFAPTLENK EKELANGRLA M LAFLGFLV ...String:
KGSWLPGLQS PAYLDGSLAG DNGFDPLALA EDPEDLRWFV QAELVNGRWA MLGVAGMLIP EVLTKAGLLN APEWYDAGKE TYFASSSTL FVIEFILFHY VEIRRWQDIK NPGSVNQDPI FKSYSLPPHE CGYPGSVFNP LNFAPTLENK EKELANGRLA M LAFLGFLV QHNVTGKGPF ENLQQHLADP WHNTIIQTI

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Macromolecule #15: Chlorophyll a-b binding protein Lhca6

MacromoleculeName: Chlorophyll a-b binding protein Lhca6 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 23.90416 KDa
SequenceString: TVCEPLGPDR PVWFPGTAPP PWLDGSLPGD FGFDPLGFGS EPESLRWFAQ AELMHGRWAM LAVAGILIPE ILQKWGFMEE FSWYTAGER EYFADPWTLF VTQMALMGWV EGRRWMDYLN PGSVDIEPRF PNRKNPTPDV GYPGGLWFDW GNWGRGSPEP V MVLRTKEI ...String:
TVCEPLGPDR PVWFPGTAPP PWLDGSLPGD FGFDPLGFGS EPESLRWFAQ AELMHGRWAM LAVAGILIPE ILQKWGFMEE FSWYTAGER EYFADPWTLF VTQMALMGWV EGRRWMDYLN PGSVDIEPRF PNRKNPTPDV GYPGGLWFDW GNWGRGSPEP V MVLRTKEI KNGRLAMLAF VGFWFQVVYT GQGPLDNLFA HLADPGHCNI FSA

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Macromolecule #16: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 16 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER / Chlorophyll a

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Macromolecule #17: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 17 / Number of copies: 137 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #18: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 18 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

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Macromolecule #19: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 19 / Number of copies: 5 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #20: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 20 / Number of copies: 25 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

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Macromolecule #21: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 21 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #22: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 22 / Number of copies: 2 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 23 / 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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Macromolecule #24: (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: 24 / Number of copies: 6 / 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 / Lutein

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Macromolecule #25: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 25 / Number of copies: 11 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

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Macromolecule #26: (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: 26 / Number of copies: 2 / 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 / Violaxanthin

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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 / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 2.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103844

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