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- EMDB-30420: Structure of the far-red light utilizing photosystem I of Acaryoc... -

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Basic information

Entry
Database: EMDB / ID: EMD-30420
TitleStructure of the far-red light utilizing photosystem I of Acaryochloris marina
Map dataPostprocess_masked.mrc
Sample
  • Complex: Photosystem I complex from Acaryochloris marina
    • Protein or peptide: x 11 types
  • Ligand: x 9 types
KeywordsPhotosynthesis / Photosystem I / Acaryochloris marina / Light-harvesting / Chlorophyll d
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I reaction centre subunit PsaK superfamily / 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 PsaF, reaction centre subunit III ...Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I reaction centre subunit PsaK superfamily / 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 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 PsaB / Photosystem I PsaA / 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 P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III / Photosystem I reaction center subunit II / Photosystem I reaction center subunit PsaK / Photosystem I iron-sulfur center
Similarity search - Component
Biological speciesAcaryochloris marina (bacteria) / Acaryochloris marina MBIC11017 (bacteria) / Acaryochloris marina MBIC110017 (bacteria) / Acaryochloris marina MBIC 11017 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsKawakami K / Yonekura K
Funding support Japan, 5 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H05175 Japan
Japan Society for the Promotion of Science (JSPS)16H04757 Japan
Japan Society for the Promotion of Science (JSPS)16H06554 Japan
Japan Society for the Promotion of Science (JSPS)20K06684 Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Nat Commun / Year: 2021
Title: Structure of the far-red light utilizing photosystem I of Acaryochloris marina.
Authors: Tasuku Hamaguchi / Keisuke Kawakami / Kyoko Shinzawa-Itoh / Natsuko Inoue-Kashino / Shigeru Itoh / Kentaro Ifuku / Eiki Yamashita / Kou Maeda / Koji Yonekura / Yasuhiro Kashino /
Abstract: Acaryochloris marina is one of the cyanobacterial species that can use far-red light to drive photochemical reactions for oxygenic photosynthesis. Here, we report the structure of A. marina ...Acaryochloris marina is one of the cyanobacterial species that can use far-red light to drive photochemical reactions for oxygenic photosynthesis. Here, we report the structure of A. marina photosystem I (PSI) reaction center, determined by cryo-electron microscopy at 2.58 Å resolution. The structure reveals an arrangement of electron carriers and light-harvesting pigments distinct from other type I reaction centers. The paired chlorophyll, or special pair (also referred to as P740 in this case), is a dimer of chlorophyll d and its epimer chlorophyll d'. The primary electron acceptor is pheophytin a, a metal-less chlorin. We show the architecture of this PSI reaction center is composed of 11 subunits and we identify key components that help explain how the low energy yield from far-red light is efficiently utilized for driving oxygenic photosynthesis.
History
DepositionAug 5, 2020-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0064
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0064
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7coy
  • Surface level: 0.0055
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7coy
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_30420.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocess_masked.mrc
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.00637 / Movie #1: 0.0064
Minimum - Maximum-0.046826307 - 0.07514111
Average (Standard dev.)0.000021081954 (±0.0014213339)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 356.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z330330330
origin x/y/z0.0000.0000.000
length x/y/z356.400356.400356.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS330330330
D min/max/mean-0.0470.0750.000

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Supplemental data

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Sample components

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Entire : Photosystem I complex from Acaryochloris marina

EntireName: Photosystem I complex from Acaryochloris marina
Components
  • Complex: Photosystem I complex from Acaryochloris marina
    • 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 protein PsaD
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I protein PsaF
    • Protein or peptide: Photosystem I protein Psa27
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit PsaK
    • Protein or peptide: Photosystem I protein PsaL
    • Protein or peptide: Photosystem I protein PsaM
  • Ligand: CHLOROPHYLL D ISOMER
  • Ligand: PHEOPHYTIN A
  • Ligand: CHLOROPHYLL D
  • Ligand: UNKNOWN LIGAND
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: water

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Supramolecule #1: Photosystem I complex from Acaryochloris marina

SupramoleculeName: Photosystem I complex from Acaryochloris marina / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Acaryochloris marina (bacteria)

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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: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 83.470539 KDa
SequenceString: MTTSPGGPET KGRTAEVDIN PVSASLEVAG KPGHFNKSLS KGPQTTTWIW NLHALAHDFD TQTNDLEEIS RKIFSAHFGH LSIIFVWIS GMIFHAARFS NYYAWLADPL GNKPSAHVVW PIVGQDILNA DVGNGFRGVQ ITSGLFHILR GAGMTDPGEL Y SAAIGALV ...String:
MTTSPGGPET KGRTAEVDIN PVSASLEVAG KPGHFNKSLS KGPQTTTWIW NLHALAHDFD TQTNDLEEIS RKIFSAHFGH LSIIFVWIS GMIFHAARFS NYYAWLADPL GNKPSAHVVW PIVGQDILNA DVGNGFRGVQ ITSGLFHILR GAGMTDPGEL Y SAAIGALV AAVVMMYAGY YHYHKKAPKL EWFQNAESTM THHLIVLLGL GNLAWTGHLI HVSLPVNKLL DSGVAPQDIP IP HEFLFDN GFMADLYPSF AQGLMPYFTL NWGAYSDFLT FKGGLDPTTG GLWMTDIAHH HLALAVMYII AGHMYRTNWG IGH SMKEIM ESHKGPFTGE GHKGLYEVLT TSWHAQLAIN LATWGSFSII VAHHMYAMPP YPYLATDYGT QLNLFVHHMW IGGF LIVGG AAHAAIFMVR DYDPAVNQNN VLDRMLRHRD TIISHLNWVC IFLGFHSFGL YIHNDNMRSL GRPQDMFSDT AIQLQ PIFS QWVQNLQANV AGTIRAPLAE GASSLAWGGD PLFVGGKVAM QHVSLGTADF MIHHIHAFQI HVTVLILIKG VLYARS SRL IPDKANLGFR FPCDGPGRGG TCQSSGWDHI FLGLFWMYNC ISIVNFHFFW KMQSDVWGAA NANGGVNYLT AGNWAQS SI TINGWLRDFL WAQSVQVINS YGSALSAYGI LFLGAHFIWA FSLMFLFSGR GYWQELIESI VWAHSKLKIA PAIQPRAM S ITQGRAVGLG HYLLGGIVTS WSFYLARILA LG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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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: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Acaryochloris marina MBIC110017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 82.210555 KDa
SequenceString: MATKFPSFSQ DLAQDPTTRR IWYGIATVHD FETHDGMTEE NLYQKIFATH FGHLSIIFLW SAGHLFHVAW QGNFEQWIQD PLTIRPIAH AIWDPHLGDA ATQAFTQAGA SGPVDLCYSG LYQWWYTIGM RTNGDLYIGS VFLMIVAAVM LFAGWLHLQP K FRPSLAWF ...String:
MATKFPSFSQ DLAQDPTTRR IWYGIATVHD FETHDGMTEE NLYQKIFATH FGHLSIIFLW SAGHLFHVAW QGNFEQWIQD PLTIRPIAH AIWDPHLGDA ATQAFTQAGA SGPVDLCYSG LYQWWYTIGM RTNGDLYIGS VFLMIVAAVM LFAGWLHLQP K FRPSLAWF RDAESQMNHH LAVLFGASSL GWTGHLIHVA IPEARGQHVG WDNFLSTMPH PAGLAPFFTG RWGVYAQNPD TA GHIFGTS EGAGTAIITF IGGFHPQTEA LWLTDIAHHH LAIAVMYIIA GHMYRTQFGI GHSMKEILEA HTPPSGMLGD AHK GLYDTY NESLHFQLGF HLAALGVITS VVAQHMYSLP SYAFISQDHV TQAALYTHHQ YIAGILAIGA FAHGGIFFVR DYDP ERNKN NVLARALEHK EAIISHLSWV SMFSGFHTLG VYVHNDTVVA FGTPEKQILV EPIFAQWIQA AHGKLLLGFE TLLSN PNGL AYNPPNISPD VFVPGWVEAM NNPVIGPFMS QGPGDFLVHH GIAFSLHVTV LICVKGCLDA RGSKLMPDKK DFGYSF PCD GPGRGGTCDI SAWDSFYLAF FWMLNTIGWI VFYFNWKHLA IWSGNEAQFN TNSTYLMGWL RDYLWGYSAQ LINGYTP FG VNSLSVWAWI FLLGHLCWAT GFLFLISWRG YWQELIETLV WAHQRTPLAN LVTWKDKPVA LSIVQGRLVG LVHFAVGY Y VTYAAFVIGA TAPLG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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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: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Acaryochloris marina MBIC110017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 8.825207 KDa
SequenceString:
MSHTVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCKAGQIA SSPRTEDCVG CKRCETACPT DFLSIRVYLG AETTRSMGLA Y

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #4: Photosystem I protein PsaD

MacromoleculeName: Photosystem I protein PsaD / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC110017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 15.114146 KDa
SequenceString:
MAETLTGQTP LFGGSTGGLL SSAETEEKYA ITWTSPKQQV FEMPTGGAAV MNEGENLLYL ARKEQCLALG LRQLRTKKIM DYKIYRVLP DGSNTLLHPK DGVFPEKSNE GRAAVNSVAR SIGENPNPGA IKYTGKKAYD

UniProtKB: Photosystem I reaction center subunit II

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Macromolecule #5: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC110017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 9.560822 KDa
SequenceString:
MVQRGSKVRI LRPESYWFRE IGTVASVDQS GIKYPVIVRF DTCNYNGISG TAAGINTNNF GVHELEEVEA PKGGKKPAAK PAAAPKAEG

UniProtKB: Photosystem I reaction center subunit IV

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Macromolecule #6: Photosystem I protein PsaF

MacromoleculeName: Photosystem I protein PsaF / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC110017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 17.844621 KDa
SequenceString:
MRRLFAVLLV MTLFLGVVPP ASADIGGLVP CSESPKFQER AAKARNTTAD PNSGQKRFEM YSSALCGPED GLPRIIAGGP MRRAGDFLI PGLFFIYIAG GIGNSSRNYQ IANRKKNAKN PAMGEIIIDV PLAVSSTIAG MAWPLTAFRE LTSGELTVPD S DVTVSPR

UniProtKB: Photosystem I reaction center subunit III

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Macromolecule #7: Photosystem I protein Psa27

MacromoleculeName: Photosystem I protein Psa27 / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 3.648337 KDa
SequenceString:
MISDILPAIM TPLVVLIGGG AAMTAFFYYV EREG

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Macromolecule #8: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC110017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 5.900939 KDa
SequenceString:
MGDVPLKIDS EKDFMKFFST APVIALVFFT LTAGFLVELN RFFPDILFFP Y

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #9: Photosystem I reaction center subunit PsaK

MacromoleculeName: Photosystem I reaction center subunit PsaK / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC 11017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 9.289071 KDa
SequenceString:
MHPILLTTFE SHPWTVNTGI LMLFINLLMV FLGRYAIKYP GQGPALPIGV PDSMKDFGVP EMLATGVFAH WIGAGMILGL RSAGAL

UniProtKB: Photosystem I reaction center subunit PsaK

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Macromolecule #10: Photosystem I protein PsaL

MacromoleculeName: Photosystem I protein PsaL / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC 11017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 15.349588 KDa
SequenceString:
MTMDLVKHGG DPLVGDLATP VNSSGIVKAW INNLPAYRKG MSANARGLEI GMAHGYYLYG PFATSGPIRG TTMSLVSGVL SASAVVIVL SVAIQIYSSV SSAKPLPSVT TADPGSDFGT KEGWSAVGSG FLIGGCGGAV IAGVLSYAIA AFVG

UniProtKB: Photosystem I reaction center subunit XI

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Macromolecule #11: Photosystem I protein PsaM

MacromoleculeName: Photosystem I protein PsaM / type: protein_or_peptide / ID: 11 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 3.190899 KDa
SequenceString:
MELSDLQIVI ALVVALLPAL LALNLGSALS K

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Macromolecule #12: CHLOROPHYLL D ISOMER

MacromoleculeName: CHLOROPHYLL D ISOMER / type: ligand / ID: 12 / Number of copies: 3 / Formula: G9R
Molecular weightTheoretical: 895.462 Da
Chemical component information

ChemComp-G9R:
CHLOROPHYLL D ISOMER

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Macromolecule #13: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 13 / Number of copies: 6 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #14: CHLOROPHYLL D

MacromoleculeName: CHLOROPHYLL D / type: ligand / ID: 14 / Number of copies: 210 / Formula: CL7
Molecular weightTheoretical: 895.462 Da
Chemical component information

ChemComp-CL7:
CHLOROPHYLL D

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Macromolecule #15: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 15 / Number of copies: 36 / Formula: UNL
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #16: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 16 / Number of copies: 6 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #17: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 17 / Number of copies: 6 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #18: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 18 / Number of copies: 9 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #19: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 19 / Number of copies: 3 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #20: water

MacromoleculeName: water / type: ligand / ID: 20 / Number of copies: 84 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 6.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 85.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Startup modelType of model: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86419
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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