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- EMDB-31348: Barley photosystem I-LHCI-Lhca5 supercomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-31348
TitleBarley photosystem I-LHCI-Lhca5 supercomplex
Map data
Sample
  • Complex: PSI-LHCI-Lhca5 supercomplex of Barley
    • Protein or peptide: x 15 types
  • Ligand: x 11 types
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane ...photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / 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 / 4 iron, 4 sulfur cluster binding / : / electron transfer activity / magnesium ion binding / integral component of membrane / metal ion binding
Similarity search - Function
Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit psaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Chlorophyll A-B binding protein, plant and chromista ...Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit psaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Chlorophyll A-B binding protein, plant and chromista / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I PsaL, reaction centre subunit XI / Chlorophyll A-B binding protein / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Chlorophyll A-B binding protein / Photosystem I reaction centre subunit XI / 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 PsaJ, reaction centre subunit IX superfamily / PsaD / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA / Photosystem I PsaA/PsaB superfamily / Photosystem I PsaA/PsaB / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 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, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit VI, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit II, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I iron-sulfur center ...Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit VI, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit II, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I iron-sulfur center / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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
Citation
Journal: 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.
#1: Journal: Science / Year: 2015
Title: Photosynthesis. Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex
Authors: Qin XC / Suga M / Kuang TY / Shen JR
History
DepositionMay 24, 2021-
Header (metadata) releaseDec 22, 2021-
Map releaseDec 22, 2021-
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: 0.72
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.72
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ew6
  • Surface level: 0.72
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_31348.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 440 pix.
= 575.08 Å
1.31 Å/pix.
x 440 pix.
= 575.08 Å
1.31 Å/pix.
x 440 pix.
= 575.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.307 Å
Density
Contour LevelBy AUTHOR: 0.72 / Movie #1: 0.72
Minimum - Maximum-2.0786717 - 5.0564976
Average (Standard dev.)-0.00090195425 (±0.0821656)
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
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-2.0795.056-0.001

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Supplemental data

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Sample components

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Entire : PSI-LHCI-Lhca5 supercomplex of Barley

EntireName: PSI-LHCI-Lhca5 supercomplex of Barley
Components
  • Complex: PSI-LHCI-Lhca5 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 II, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit IV, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit III, 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: Chlorophyll a-b binding protein Lhca1
    • 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 Lhca5
  • 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-Lhca5 supercomplex of Barley

SupramoleculeName: PSI-LHCI-Lhca5 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: 83.217219 KDa
SequenceString: MIIRSPEPEV KIVVDRDPVK TSFEEWARPG HFSRTLAKGP DTTTWIWNLH ADAHDFDSHT GDLEEISRKV FSAHFGQLSI IFLWLSGMY FHGARFSNYE AWLSDPTHIG PSAQVVWPIV GQEILNGDVG GGFRGIQITS GFFQLWRASG ITSELQLYCT A IGALVFAA ...String:
MIIRSPEPEV KIVVDRDPVK TSFEEWARPG HFSRTLAKGP DTTTWIWNLH ADAHDFDSHT GDLEEISRKV FSAHFGQLSI IFLWLSGMY FHGARFSNYE AWLSDPTHIG PSAQVVWPIV GQEILNGDVG GGFRGIQITS GFFQLWRASG ITSELQLYCT A IGALVFAA LMLFAGWFHY HKAAPKLAWF QDVESMLNHH LAGLLGLGSL SWAGHQIHVS LPINQFLDAG VDPKEIPLPH EF ILNRDLL AQLYPSFAEG ATPFFTLNWS KYAEFLTFRG GLDPVTGGLW LTDIAHHHLA IAILFLIAGH MYRTNWGIGH GLK DILEAH KGPFTGQGHK GLYEILTTSW HAQLSLNLAM LGSTTIVVAH HMYSMPPYPY LATDYGTQLS LFTHHMWIGG FLIV GAAAH AAIFMVRDYD PTTRYNDLLD RVLRHRDAII SHLNWVCIFL GFHSFGLYIH NDTMSALGRP QDMFSDTAIQ LQPIF AQWV QNIHATAPGV TAPGATTSTS LTWGGGELVA VGGKVALLPI PLGTADFLVH HIHAFTIHVT VLILLKGVLF ARSSRL IPD KANLGFRFPC DGPGRGGTCQ VSAWDHVFLG LFWMYNAISV VIFHFSWKMQ SDVWGTISDQ GVVTHITGGN FAQSSIT IN GWLRDFLWAQ ASQVIQSYGS SLSAYGLFFL GAHFVWAFSL MFLFSGRGYW QELIESIVWA HNKLKVAPAT QPRALSII Q GRAVGVTHYL LGGIATTWAF FLARIIAVG

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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: 82.693914 KDa
SequenceString: MELRFPRFSQ GLAQDPTTRR IWFGIATAHD FESHDDITEE RLYQNIFASH FGQLAIIFLW TSGNLFHVAW QGNFESWIQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA AGPVNIAYSG VYQWWYTIGL RTNEDLYTGA LFLLFLSTLS LIASWLHLQP K WKPSLSWF ...String:
MELRFPRFSQ GLAQDPTTRR IWFGIATAHD FESHDDITEE RLYQNIFASH FGQLAIIFLW TSGNLFHVAW QGNFESWIQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA AGPVNIAYSG VYQWWYTIGL RTNEDLYTGA LFLLFLSTLS LIASWLHLQP K WKPSLSWF KNAESRLNHH LSGLFGVSSL AWTGHLVHVA IPASRGEYVR WNNFLDVLPY PQGLGPLLTG QWNLYAQNPD SS NHLFGTA QGAGTAILTL LGGFHPQTQS LWLTDMAHHH LAIAFIFLIA GHMYRTNFGI GHSIKDLLEA HTPPGGRLGR GHK GLYDTI NNSIHFQLGL ALASLGVITS LVAQHMYSLP PYAFIAQDFT TQAALYTHHQ YIAGFIMTGA FAHGAIFFIR DYNP EQNED NVLARMLDHK EAIISHLSWA SLFLGFHTLG LYVHNDVMLA FGTPEKQILI EPIFAQWIQS AHGKTTYGFD ILLSS TNGP AFNAGRSLWL PGWLNAVNEN SNSLFLTIGP GDFLVHHAIA LGLHTTTLIL VKGALDARGS KLMPDKKDFG YSFPCD GPG RGGTCDISAW DAFYLAVFWM LNTIGWVTFY WHWKHITLWQ GNVSQFNESS TYLMGWLRDY LWLNSSQLIN GYNPFGM NS LSVWAWMFLF GHLVWATGFM FLISWRGYWQ ELIETLAWAH ERTPLANLIR WRDKPVALSI VQARLVGLAH FSVGYIFT Y AAFLIASTSG KFG

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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 / EC number: photosystem I
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 II, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit II, chloroplastic
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 21.958137 KDa
SequenceString: MAMATQASAA TRHLITAAWS PSAKPRPATL AMPSSARGPA PLFAAAPDTP APAAPPAEPA PAGFVPPQLD PSTPSPIFGG STGGLLRKA QVEEFYVITW TSPKEQVFEM PTGGAAIMRE GPNLLKLARK EQCLALGNRL RSKYKIAYQF YRVFPNGEVQ Y LHPKDGVY ...String:
MAMATQASAA TRHLITAAWS PSAKPRPATL AMPSSARGPA PLFAAAPDTP APAAPPAEPA PAGFVPPQLD PSTPSPIFGG STGGLLRKA QVEEFYVITW TSPKEQVFEM PTGGAAIMRE GPNLLKLARK EQCLALGNRL RSKYKIAYQF YRVFPNGEVQ Y LHPKDGVY PEKVNAGRQG VGQNFRSIGK NVSPIEVKFT GKNSFDI

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Macromolecule #5: Photosystem I reaction center subunit IV, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit IV, chloroplastic
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 15.476541 KDa
SequenceString:
MASTNMASAT SRFMLAAGIP SGANGGVSSR VSFLPSNRLG LKLVARAEEP TAAAPAEPAP AADEKPEAAV ATKEPAKAKP PPRGPKRGT KVKILRRESY WYNGTGSVVT VDQDPNTRYP VVVRFAKVNY AGVSTNNYAL DEIKEVAA

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

MacromoleculeName: Photosystem I reaction center subunit III, chloroplastic
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 24.866574 KDa
SequenceString: MAALAASIAT STAFAAKPRL SRPPARLSVS CSASSGDNNN STATPSLSAS IKTFSAALAL SSVLLSSAAT SPPPAAADIA GLTPCKESK AFAKREKQSV KKLNSSLKKY APDSAPALAI QATIDKTKRR FENYGKFGLL CGSDGLPHLI VSGDQRHWGE F ITPGVLFL ...String:
MAALAASIAT STAFAAKPRL SRPPARLSVS CSASSGDNNN STATPSLSAS IKTFSAALAL SSVLLSSAAT SPPPAAADIA GLTPCKESK AFAKREKQSV KKLNSSLKKY APDSAPALAI QATIDKTKRR FENYGKFGLL CGSDGLPHLI VSGDQRHWGE F ITPGVLFL YIAGWIGWVG RSYLIAVSGE KKPAMREIII DVELAARIIP RGFIWPVAAY RELINGDLVV DDADIGY

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 14.900113 KDa
SequenceString:
MASLVAVQPA AVKGLSGSSI SGRKLAVRPS SAAVSRSTRR ARGAAVVAKY GEKSVYFDLD DIANTTGQWD LYGSDAPSPY NGLQSKFFN TFAAPFTKRG LLLKFLLIGG GSLVAYVSAS ASPDLLPIKK GPQLPPTPGP RGKI

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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: 4.010949 KDa
SequenceString:
MTDLNLPSIF VPLVGLVFPA IAMTSLFLYV QKKKIV

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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 psaK, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit psaK, chloroplastic
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 13.742934 KDa
SequenceString:
MASQLSAMTS VPQFHGLRTY SSPRSMATLP SLRRRRSQGI RCDYIGSSTN LIMVTTTTLM LFAGRFGLAP SANRKATAGL KLEARESGL QTGDPAGFTL ADTLACGAVG HIMGVGIVLG LKNTGVLDQI IG

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

MacromoleculeName: Photosystem I reaction center subunit XI, chloroplastic
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 22.22973 KDa
SequenceString: MATAYAPPMA SQVMKSGLAC SKPRGMSGAS LTRRPRFVVK AVKSDKPTYQ VVQPINGDPF IGSLETPVTS SPLVAWYLSN LPAYRTAVS PLLRGIEVGL AHGYLLVGPF ALTGPLRNTP VHGQAGTLGA IGLVSILSVC LTMYGVASFN EGEPSTAPVL T LTGRKKEA ...String:
MATAYAPPMA SQVMKSGLAC SKPRGMSGAS LTRRPRFVVK AVKSDKPTYQ VVQPINGDPF IGSLETPVTS SPLVAWYLSN LPAYRTAVS PLLRGIEVGL AHGYLLVGPF ALTGPLRNTP VHGQAGTLGA IGLVSILSVC LTMYGVASFN EGEPSTAPVL T LTGRKKEA DKLQTAEGWS QFTGGFFFGG VSGAVWAYFL LYVLDLPYFF K

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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: 26.691438 KDa
SequenceString: MAMASSSGLR SCSAVGVPSL LAPSSRSGRS GLPFCAYATT SGRVTMSAEW FPGQPRPAHL DGSSPGDFGF DPLGLATVPE NFERFKESE IYHCRWAMLC VPGVLVPEAL GLGNWVKAQE WAALPDGQAT YLGNPVPWGN LPTILAIEFL AIAFAEQQRT M EKDPEKKK ...String:
MAMASSSGLR SCSAVGVPSL LAPSSRSGRS GLPFCAYATT SGRVTMSAEW FPGQPRPAHL DGSSPGDFGF DPLGLATVPE NFERFKESE IYHCRWAMLC VPGVLVPEAL GLGNWVKAQE WAALPDGQAT YLGNPVPWGN LPTILAIEFL AIAFAEQQRT M EKDPEKKK YPGGAFDPLG FSKDPAKFEE LKLKEIKNGR LAMLAFVGFC VQQSAYPGTG PLENLATHLA DPWHNNIGDI VI PRNIYGP

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 27.320039 KDa
SequenceString: MALVSSSSAT AVAALPSNGL AGARTSFLGA AGKAAASRTS FAVRAAAPER PIWFPGSTPP PWLDGSLPGD FGFDPWGLGS DPESLRWNV QAELVHCRWA MLGAAGIFIP ELLTKIGILN TPSWYTAGEQ EYFTDTTTLF IVELILIGWA EGRRWADIIK P GCVNTDPI ...String:
MALVSSSSAT AVAALPSNGL AGARTSFLGA AGKAAASRTS FAVRAAAPER PIWFPGSTPP PWLDGSLPGD FGFDPWGLGS DPESLRWNV QAELVHCRWA MLGAAGIFIP ELLTKIGILN TPSWYTAGEQ EYFTDTTTLF IVELILIGWA EGRRWADIIK P GCVNTDPI FPNNKLTGTD VGYPGGLWFD PLGYGTGSPE KLKELRTKEI KNGRLAMLAV MGAWFQAEYT GTGPIDNLFA HL ADPGHAT IFRAFAPK

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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 subsp. spontaneum (wild barley)
Molecular weightTheoretical: 29.374547 KDa
SequenceString: MAAQGLLSGR QLLGRPLQSS FSRSSSSRKS PFVVRASSSP PAKQNDNRQL WFASKQSLTY LDGTLPGDFG FDPLGLSDPE GTGGFIEPR WLAYGEIFNG RTAMMGVVGM IAPEALGKVG LVPPETAIPW FQAGAIPPAG TYQYWADPYT LFVFEMALIG F AEHRRLQD ...String:
MAAQGLLSGR QLLGRPLQSS FSRSSSSRKS PFVVRASSSP PAKQNDNRQL WFASKQSLTY LDGTLPGDFG FDPLGLSDPE GTGGFIEPR WLAYGEIFNG RTAMMGVVGM IAPEALGKVG LVPPETAIPW FQAGAIPPAG TYQYWADPYT LFVFEMALIG F AEHRRLQD WYNPGSMGKQ YFLGLEKYLG GSGDPAYPGG PIFNPLGFGT KSEKEMKELK LKEIKNGRLA MLAFLGMSLQ AI FTGVGPF QNLLDHLSDP VNNNILTSLK FH

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Macromolecule #15: Chlorophyll a-b binding protein Lhca5

MacromoleculeName: Chlorophyll a-b binding protein Lhca5 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Molecular weightTheoretical: 27.618691 KDa
SequenceString: MALAANAHGR VCTLSSRPPA PFSSRSTVAM PGHHSESPRA RFAVRAIAER ATWLPGLDPP AYLDGTLPGD YGFDPLGLGE QPEDLKWYV QAELVHCRFA MAGVAGILGT DLIRVSGIGN LPVWFEAGAT KFDFANTTAL FFVQLLLMGF VETKRYMDFV S PGSQAKEG ...String:
MALAANAHGR VCTLSSRPPA PFSSRSTVAM PGHHSESPRA RFAVRAIAER ATWLPGLDPP AYLDGTLPGD YGFDPLGLGE QPEDLKWYV QAELVHCRFA MAGVAGILGT DLIRVSGIGN LPVWFEAGAT KFDFANTTAL FFVQLLLMGF VETKRYMDFV S PGSQAKEG TFLGIEASLE GLQPGYPGGP LFNPMGLAKD IENANEVKLK EIKNGRLAMV AMLGFIVQAS VTHAGPIDNL LT HLSDPFN KNIIHALTLS

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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: 136 / 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: 5 / 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: 12 / 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
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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103844

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