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- EMDB-9854: Structure of the green algal photosystem I supercomplex with ligh... -

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Basic information

Entry
Database: EMDB / ID: EMD-9854
TitleStructure of the green algal photosystem I supercomplex with light-harvesting complex I
Map data
Sample
  • Complex: Photosystem I - Light Harvesting Complex I supercomplex
    • Protein or peptide: x 18 types
  • Ligand: x 10 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 / metal ion binding
Similarity search - Function
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 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 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 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 / 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 / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / 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 VIII / PSI subunit V / Chlorophyll a-b binding protein, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit IX ...Photosystem I reaction center subunit VIII / PSI subunit V / Chlorophyll a-b binding protein, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit II, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSuga M / Miyazaki N / Takahashi Y
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP16H06554 Japan
Japan Society for the Promotion of ScienceJP16H06296 Japan
Japan Society for the Promotion of ScienceJP16H06162 Japan
CitationJournal: Nat Plants / Year: 2019
Title: Structure of the green algal photosystem I supercomplex with a decameric light-harvesting complex I.
Authors: Michihiro Suga / Shin-Ichiro Ozawa / Kaori Yoshida-Motomura / Fusamichi Akita / Naoyuki Miyazaki / Yuichiro Takahashi /
Abstract: In plants and green algae, the core of photosystem I (PSI) is surrounded by a peripheral antenna system consisting of light-harvesting complex I (LHCI). Here we report the cryo-electron ...In plants and green algae, the core of photosystem I (PSI) is surrounded by a peripheral antenna system consisting of light-harvesting complex I (LHCI). Here we report the cryo-electron microscopic structure of the PSI-LHCI supercomplex from the green alga Chlamydomonas reinhardtii. The structure reveals that eight Lhca proteins form two tetrameric LHCI belts attached to the PsaF side while the other two Lhca proteins form an additional Lhca2/Lhca9 heterodimer attached to the opposite side. The spatial arrangement of light-harvesting pigments reveals that Chlorophylls b are more abundant in the outer LHCI belt than in the inner LHCI belt and are absent from the core, thereby providing the downhill energy transfer pathways to the PSI core. PSI-LHCI is complexed with a plastocyanin on the patch of lysine residues of PsaF at the luminal side. The assembly provides a structural basis for understanding the mechanism of light-harvesting, excitation energy transfer of the PSI-LHCI supercomplex and electron transfer with plastocyanin.
History
DepositionMar 20, 2019-
Header (metadata) releaseJun 19, 2019-
Map releaseJun 19, 2019-
UpdateJun 26, 2019-
Current statusJun 26, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jo6
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9854.png

Downloads & links

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Map

FileDownload / File: emd_9854.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.12 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.22062866 - 0.46019447
Average (Standard dev.)0.0008142805 (±0.010991188)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 358.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ858858858
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.2210.4600.001

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Supplemental data

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Sample components

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Entire : Photosystem I - Light Harvesting Complex I supercomplex

EntireName: Photosystem I - Light Harvesting Complex I supercomplex
Components
  • Complex: Photosystem I - Light Harvesting Complex I supercomplex
    • 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 F, Photosystem I reaction center subunit III, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit V, 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
    • 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: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • 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: CHLOROPHYLL B
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Supramolecule #1: Photosystem I - Light Harvesting Complex I supercomplex

SupramoleculeName: Photosystem I - Light Harvesting Complex I supercomplex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 83.239203 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: MTISTPEREA KKVKIAVDRN PVETSFEKWA KPGHFSRTLS KGPNTTTWIW NLHADAHDFD SHTSDLEEIS RKVFSAHFGQ LGIIFIWLS GMYFHGARFS NYEAWLSDPT HIKPSAQVVW PIVGQEILNG DVGGGFQGIQ ITSGFFQLWR ASGITSELQL Y TTAIGGLV ...String:
MTISTPEREA KKVKIAVDRN PVETSFEKWA KPGHFSRTLS KGPNTTTWIW NLHADAHDFD SHTSDLEEIS RKVFSAHFGQ LGIIFIWLS GMYFHGARFS NYEAWLSDPT HIKPSAQVVW PIVGQEILNG DVGGGFQGIQ ITSGFFQLWR ASGITSELQL Y TTAIGGLV MAAAMFFAGW FHYHKAAPKL EWFQNVESML NHHLGGLLGL GSLAWAGHQI HVSLPVNKLL DAGVDPKEIP LP HDLLLNR AIMADLYPSF AKGIAPFFTL NWSEYSDFLT FKGGLNPVTG GLWLSDTAHH HVAIAVLFLV AGHMYRTNWG IGH SMKEIL EAHRGPFTGE GHVGLYEILT TSWHAQLAIN LALFGSLSII VAHHMYAMPP YPYLATDYGT QLSLFTHHTW IGGF CIVGA GAHAAIFMVR DYDPTNNYNN LLDRVIRHRD AIISHLNWVC IFLGFHSFGL YIHNDTMSAL GRPQDMFSDT AIQLQ PVFA QWIQNTHFLA PQLTAPNALA ATSLTWGGDL VAVGGKVAMM PISLGTSDFM VHHIHAFTIH VTVLILLKGV LFARSS RLI PDKANLGFRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNSL SIVIFHFSWK MQSDVWGTVT ASGVSHITGG NFAQSAN TI NGWLRDFLWA QSSQVIQSYG SALSAYGLIF LGAHFVWAFS LMFLFSGRGY WQELIESIVW AHNKLKVAPA IQPRALSI T QGRAVGVAHY LLGGIATTWS FFLARIISVG

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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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 84.947195 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: MATHHHHHHH HHHHHHHHHH HHHKLFPKFS QGLAQDPTTR RIWYGLAMAH DFESHDGMTE ENLYQKIFAS HFGQLSIIFL WTSGNLFHV AWQGNFEQWV TDPVHIRPIA HAIWDPHFGQ PAVEAFTRGG ASGPVNISTS GVYQWWYTIG MRTNQDLYVG S VFLALVSA ...String:
MATHHHHHHH HHHHHHHHHH HHHKLFPKFS QGLAQDPTTR RIWYGLAMAH DFESHDGMTE ENLYQKIFAS HFGQLSIIFL WTSGNLFHV AWQGNFEQWV TDPVHIRPIA HAIWDPHFGQ PAVEAFTRGG ASGPVNISTS GVYQWWYTIG MRTNQDLYVG S VFLALVSA IFLFAGWLHL QPNFQPSLSW FKDAESRLNH HLSGLFGVSS LAWTGHLVHV AIPESRGQHV GWDNFLSVLP HP QGLTPFF TGNWAAYAQS PDTASHVFGT AQGSGQAILT FLGGFHPQTQ SLWLTDMAHH HLAIAVIFIV AGHMYRTNFG IGH RMQAIL EAHTPPSGSL GAGHKGLFDT VNNSLHFQLG LALASVGTIT SLVAQHMYSL PPYAFQAIDF TTQAALYTHH QYIA GFIMC GAFAHGAIFF IRDYDPEQNK GNVLARMLDH KEALISHLSW VSLFLGFHTL GLYVHNDVMQ AFGTPEKQIL IEPVF AQWI QAAHGKALYG FDFLLSSKTS AAFANGQSLW LPGWLDAINN NQNSLFLTIG PGDFLVHHAI ALGLHTTTLI LVKGAL DAR GSKLMPDKKD FGYSFPCDGP GRGGTCDISA YDAFYLAVFW MLNTIGWVTF YWHWKHLTLW QGNVAQFDES STYLMGW LR DYLWLNSSQL INGYNPFGMN SLSVWAWTFL FGHLIYATGF MFLISWRGYW QELIETLVWA HEKTPLANLV YWKDKPVA L SIVQARLVGL AHFSVGYIFT YAAFLIASTS GRFG

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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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 8.869325 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString:
MAHIVKIYDT CIGCTQCVRA CPLDVLEMVP WDGCKASQMA SAPRTEDCVG CKRCETACPT DFLSVRVYLG SESTRSMGLS 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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 17.732496 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString:
EAEAAPAAAK KAAEKPAWTV PTLNPDTPSP IFGGSTGGLL RKAQTEEFYV ITWEAKKEQI FEMPTGGAAI MRQGPNLLKF GKKEQCLAL TTQLRNKFKL TPCFYRVFPD GKVQYLHPAD GVYPEKVNAG RVGANQNMRR IGQNVNPIKV KFSGRMMSPA E I

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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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 8.135226 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString:
EEVKAAPKKE VGPKRGSLVK ILRPESYWFN QVGKVVSVDQ SGVRYPVVVR FENQNYAGVT TNNYALDEVV AAK

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Macromolecule #6: Photosystem I reaction center subunit F, Photosystem I reaction c...

MacromoleculeName: Photosystem I reaction center subunit F, Photosystem I reaction center subunit III, chloroplastic
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 17.957773 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString:
DIAGLTPCSE SKAYAKLEKK ELKTLEKRLK QYEADSAPAV ALKATMERTK ARFANYAKAG LLCGNDGLPH LIADPGLALK YGHAGEVFI PTFGFLYVAG YIGYVGRQYL IAVKGEAKPT DKEIIIDVPL ATKLAWQGAG WPLAAVQELQ RGTLLEKEEN I TVSPR

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

MacromoleculeName: Photosystem I reaction center subunit V, chloroplastic
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 9.828936 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString:
ALDPQIVISG STAAFLAIGR FVFLGYQRRE ANFDSTVGPK TTGATYFDDL QKNSTIFATN DPAGFNIIDV AGWGALGHAV GFAVLAINS LQGAN

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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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 10.586388 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString:
MALRAVSAKS AVRPTVARAS VKPVAALKPA QKMALAGAAS VALLAASSSS AEASQVIATV ASAAQGYPFV PPSWAPSVFV PLTGLVLPA IAMATLFVYI EKEAPSS

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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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.750509 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString:
MKDFTTYLST APVIATIWFT FTAGLLIEIN RYFPDPLVFS F

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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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 8.431764 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString:
DGFIGSSTNL IMVASTTATL AAARFGLAPT VKKNTTAGLK LVDSKNSAGV ISNDPAGFTI VDVLAMGAAG HGLGVGIVLG LKGIGAL

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Macromolecule #11: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 16.120512 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString:
QVISPVNGDP FVGMLETPVT SAPIVATYLS NLPAYRTGVA PVLRGVEIGL AHGFLLAGPF IKLGPLRNVP ETAEIAGSLS AAGLVLILA LCLSIYGSAQ FQSTPSIGVK TLSGRSVARD PLFSADGWSE FAAGFLVGGE AGVAWAYVCT QILPYYS

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Macromolecule #12: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 20.368023 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: KAGNWLPGSD APAWLPDDLP GNYGFDPLSL GKEPASLKRF TESEVIHGRW AMLGVAGSLA VELLGYGNWY DAPLWAVNGG KATWFGIEV PFDLNALLAF EFVAMAAAEG QRGDAGGVVY PGGAFDPLGF AKDSSKSGEL KLKEIKNGRL AMVAFLGFVA Q HAATGKGP ...String:
KAGNWLPGSD APAWLPDDLP GNYGFDPLSL GKEPASLKRF TESEVIHGRW AMLGVAGSLA VELLGYGNWY DAPLWAVNGG KATWFGIEV PFDLNALLAF EFVAMAAAEG QRGDAGGVVY PGGAFDPLGF AKDSSKSGEL KLKEIKNGRL AMVAFLGFVA Q HAATGKGP IAALGEHLAN PWGANFATNG ISVPFF

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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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 29.435598 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: EEKSIAKVDR SKDQLYVGAS QSSLAYLDGS LPGDFGFDPL GLLDPVNSGG FIEPKWLQYS EVIHARWAML GAAGCIAPEV LGAAGLIPD ATNIKWFESG VIPPAGSYNG YWADPYTIFF VEIVAMQFAE LRRLQDFRYP GSMGQQYFLG LEAIFKGSGD A AYPGGPFF ...String:
EEKSIAKVDR SKDQLYVGAS QSSLAYLDGS LPGDFGFDPL GLLDPVNSGG FIEPKWLQYS EVIHARWAML GAAGCIAPEV LGAAGLIPD ATNIKWFESG VIPPAGSYNG YWADPYTIFF VEIVAMQFAE LRRLQDFRYP GSMGQQYFLG LEAIFKGSGD A AYPGGPFF NLFNLGKTEA AMKELKLKEI KNGRLAMLAM LGYGAQAVMT GKGPFQNLVE HLADPVNNNI LTNFAGRVSG SS QPWRPHG WWRRRYRSVA ALALIRNRSV C

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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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 23.446553 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: AAVRPVWFPG NPPPAHLDGS LAGDYGFDPL FLGQEPQTLK WYVQAELVHG RFAMLGAAGI ILTSIGAKVG LGFPEWYDAG KVVVEKNNI DFPTLMVIQF YLMGWAETKR WYDFKNPGSQ ADGSFLGFTE EFKGLENGYP GGRFFDPMGL SRGDAAKYQE Y KQKEVKNG ...String:
AAVRPVWFPG NPPPAHLDGS LAGDYGFDPL FLGQEPQTLK WYVQAELVHG RFAMLGAAGI ILTSIGAKVG LGFPEWYDAG KVVVEKNNI DFPTLMVIQF YLMGWAETKR WYDFKNPGSQ ADGSFLGFTE EFKGLENGYP GGRFFDPMGL SRGDAAKYQE Y KQKEVKNG RLAMIACLGF AAQYAATGKG PLDNLADHLA DPNHVNFATN GVSIPIA

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 23.293613 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: RQSWLPGSQI PAHLDTPAAQ ALAGNFGFDP LGLGKDPVAL RWYQQAELIH CRTAMAGVAG ILIPGLLTKA GALNVPEWYD AGKVAIENS FAPWGSLLAV QLFLCGFVEA KRWQDIRKPG SQGEPGSFLG FEASLKGTSE LGYPGGPFDP LGLSKEADKW A DWKLKEVK ...String:
RQSWLPGSQI PAHLDTPAAQ ALAGNFGFDP LGLGKDPVAL RWYQQAELIH CRTAMAGVAG ILIPGLLTKA GALNVPEWYD AGKVAIENS FAPWGSLLAV QLFLCGFVEA KRWQDIRKPG SQGEPGSFLG FEASLKGTSE LGYPGGPFDP LGLSKEADKW A DWKLKEVK NGRLAMLAFL GFVAQKYATG AGPVDNLAAH LKDPWHVNYA TNGVSLPFL

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 25.906434 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: SAVPENVKEA REWIDAWKSK SGGAKRDAAL PSWMPGADLP GYLNGTLPGD FGFDPLYLGQ DPVKLKWYAQ AELMNARFAM LAVAGILVP ELLSNIGFSW PGAGVAWYDA GKFEYFAPAS SLFGVQMLLF AWVEIRRYQD FVKPGSANQD PIFTNNKLPD G NEPGYPGG ...String:
SAVPENVKEA REWIDAWKSK SGGAKRDAAL PSWMPGADLP GYLNGTLPGD FGFDPLYLGQ DPVKLKWYAQ AELMNARFAM LAVAGILVP ELLSNIGFSW PGAGVAWYDA GKFEYFAPAS SLFGVQMLLF AWVEIRRYQD FVKPGSANQD PIFTNNKLPD G NEPGYPGG IFDPFGWSKG DIKSLKLKEI KNGRLAMLAF AGFIGQAYTT GTTPLKNLST HLADPWSTTV WQNDLARL

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Macromolecule #17: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 25.264959 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: AADRKLWAPG VVAPEYLKGD LAGDYGWDPL GLGADPTALK WYRQSELQHA RWAMLGVAGV LVQEIVKPDV YFYEAGLPQN LPEPFTNIN MGGLLAWEFI LMHWVEVRRW QDYKNFGSVN EDPIFKGNKV PNPEMGYPGG IFDPFGFSKG NLKELQTKEI K NGRLAMIA ...String:
AADRKLWAPG VVAPEYLKGD LAGDYGWDPL GLGADPTALK WYRQSELQHA RWAMLGVAGV LVQEIVKPDV YFYEAGLPQN LPEPFTNIN MGGLLAWEFI LMHWVEVRRW QDYKNFGSVN EDPIFKGNKV PNPEMGYPGG IFDPFGFSKG NLKELQTKEI K NGRLAMIA YMAFILQAQA TGKGPLAALS AHLSNPFGNN ILKNIGTCTV PHSVDVQGLT IPLTCLWPGS Q

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Macromolecule #18: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 25.183152 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: ASSRPLWLPG STPPAHLKGD LPGDFGFDPL GLGANAESLK WFKESELVHS RWAMAAVAGI LVQEIVRPDV FWYNAGKEVE SPLGPLGLL AVEFFLMHWV EVRRWQDLRK PGSVDQDPIF SQYKLPPHEV GYPGGVFAPF IPGDLAELKV KEIKNGRLAM L AFVGFVMA ...String:
ASSRPLWLPG STPPAHLKGD LPGDFGFDPL GLGANAESLK WFKESELVHS RWAMAAVAGI LVQEIVRPDV FWYNAGKEVE SPLGPLGLL AVEFFLMHWV EVRRWQDLRK PGSVDQDPIF SQYKLPPHEV GYPGGVFAPF IPGDLAELKV KEIKNGRLAM L AFVGFVMA AQVTGKGPIA ALQEHLADPW GTTIFSKAAV VPGQAVAPPC KIPASVSYKG IEIPTPCFLQ GLWP

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Macromolecule #19: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 19 / 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 #20: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 20 / Number of copies: 197 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #21: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 21 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

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Macromolecule #22: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 22 / Number of copies: 12 / 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 #23: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 23 / Number of copies: 32 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

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Macromolecule #24: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 24 / 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 #25: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 25 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #26: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 26 / Number of copies: 1 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #27: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 27 / Number of copies: 18 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

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Macromolecule #28: (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: 28 / Number of copies: 18 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.75 µm / Nominal defocus min: 1.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 2 / Number real images: 9801 / Average exposure time: 2.5 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 3 / Avg.num./class: 230000 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 379749

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