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- EMDB-62656: Cryo-EM structure of PSI-ACPI from Rhodomonas sp. NIES-2332 at 2.... -

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Basic information

Entry
Database: EMDB / ID: EMD-62656
TitleCryo-EM structure of PSI-ACPI from Rhodomonas sp. NIES-2332 at 2.08 angstroms resolution
Map data
Sample
  • Complex: Photosystem I complex binding with 14 ACPIs
    • Protein or peptide: x 27 types
  • Ligand: x 14 types
Keywordsphotosynthesis complex / PHOTOSYNTHESIS
Biological speciesRhodomonas sp. NIES-2332 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.08 Å
AuthorsZhang WY / Akita F / Shen JR
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22H04916 Japan
CitationJournal: Front Plant Sci / Year: 2025
Title: Structural analysis of PSI-ACPI and PSII-ACPII supercomplexes from a cryptophyte alga sp. NIES-2332.
Authors: Wenyue Zhang / Nozomi Yonehara / Mizuki Ishii / Haowei Jiang / Romain La Rocca / Pi-Cheng Tsai / Hongjie Li / Koji Kato / Fusamichi Akita / Jian-Ren Shen
Abstract: Light energy is converted to chemical energy by two photosystems (PSI and PSII) in complex with their light-harvesting complex proteins (LHCI and LHCII) in photosynthesis. is a member of cryptophyte ...Light energy is converted to chemical energy by two photosystems (PSI and PSII) in complex with their light-harvesting complex proteins (LHCI and LHCII) in photosynthesis. is a member of cryptophyte alga whose LHCs contain unique chlorophyll proteins (ACPs) and phycobiliproteins. We purified PSI-ACPI and PSII-ACPII supercomplexes from a cryptophyte sp. NIES-2332 and analyzed their structures at high resolutions of 2.08 Å and 2.17 Å, respectively, using cryo-electron microscopy. These structures are largely similar to those reported previously from two other species of cryptophytes, but exhibited some differences in both the pigment locations and subunit structures. A part of the antenna subunits of both photosystems is shifted compared with the previously reported structures from other species of cryptophytes, suggesting some differences in the energy transfer rates from the antenna to the PSI and PSII cores. Newly identified lipids are found to occupy the interfaces between the antennae and cores, which may be important for assembly and stabilization of the supercomplexes. Water molecules surrounding three iron-sulfur clusters of the PSI core are found in our high-resolution structure, some of which are conserved from cyanobacteria to higher plants but some are different. In addition, our structure of PSII-ACPII lacks the subunits of oxygen-evolving complex as well as the MnCaO cluster, suggesting that the cells are in the S-growth phase, yet the PSI-ACPI structure showed the binding of PsaQ, suggesting that it is in an L-phase. These results suggest that the S-phase and L-phase can co-exist in the cryptophytic cells. The high-resolution structures of both PSI-ACPIs and PSII-ACPIIs solved in this study provide a more solid structural basis for elucidating the energy transfer and quenching mechanisms in this group of the organisms.
History
DepositionDec 10, 2024-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62656.png

Downloads & links

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Map

FileDownload / File: emd_62656.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 600 pix.
= 436.2 Å		0.73 Å/pix.
x 600 pix.
= 436.2 Å		0.73 Å/pix.
x 600 pix.
= 436.2 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032
Minimum - Maximum-0.15459506 - 0.4386637
Average (Standard dev.)0.00009800071 (±0.010828212)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 436.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62656_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_62656_half_map_2.map
Projections & Slices
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Sample components

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Entire : Photosystem I complex binding with 14 ACPIs

EntireName: Photosystem I complex binding with 14 ACPIs
Components
  • Complex: Photosystem I complex binding with 14 ACPIs
    • 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
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I reaction center subunit III
    • 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 XI
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: PsaO
    • Protein or peptide: Photosystem I reaction center subunit PsaK
    • Protein or peptide: ACPI-s
    • Protein or peptide: ACPI-c
    • Protein or peptide: ACPI-a
    • Protein or peptide: ACPI-b
    • Protein or peptide: ACPI-h
    • Protein or peptide: ACPI-m,f,j
    • Protein or peptide: ACPI-e
    • Protein or peptide: ACPI-l
    • Protein or peptide: ACPI-k
    • Protein or peptide: ACPI-i
    • Protein or peptide: ACPI-d
    • Protein or peptide: ACPI-g
    • Protein or peptide: PsaR
    • Protein or peptide: ACPI-n
    • Protein or peptide: PsaQ
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyl-18-[(1R)-2,6,6-trimethylcyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohexene
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol
  • Ligand: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
  • Ligand: Chlorophyll c2
  • Ligand: water

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Supramolecule #1: Photosystem I complex binding with 14 ACPIs

SupramoleculeName: Photosystem I complex binding with 14 ACPIs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#27
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 838.458 KDa

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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
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 83.441609 KDa
SequenceString: MTISSKEQEA KKVSITVDRD PVATSFEKWA QPGHFSRTLA KGPKTTTWIW NLHADVHDFD SHTNSLEDIS RKIFSAHFGQ LSIIFLWLS GMYFHGARFS NYSAWLSNPT AVKPSAQVVW PIVGQEILNG DVGGGFQGVQ VTSGFFQIWR ASGITSEVEL Y WCALAGLL ...String:
MTISSKEQEA KKVSITVDRD PVATSFEKWA QPGHFSRTLA KGPKTTTWIW NLHADVHDFD SHTNSLEDIS RKIFSAHFGQ LSIIFLWLS GMYFHGARFS NYSAWLSNPT AVKPSAQVVW PIVGQEILNG DVGGGFQGVQ VTSGFFQIWR ASGITSEVEL Y WCALAGLL MSGLMIFAGW FHYHKAAPKL EWFQNAESML NHHLSGLLGL GCLSWAGHQI HISLPVNKLL DAGVAPQEIP LP HEFLVNR DLMAQLYPSF SKGLVPFFTL NWSEYSDFLT FKGGLNPVTG GLWLSDTAHH HLALAVLFIV AGHMYRTNWG IGH SMKEIL EAHKGPFTGE GHKGLYEILT TSWHAQLAIN LAMMGSVSII VAHHMYAMPP YPYIATDYPT QLSIFTHHMW IGGF CVVGG AAHAGIFMVR DYNPAQNYNN LLDRVIRHRD AIISHLNWIC IFLGFHSFGL YIHNDTMRAL GRTQDMFSDT AIQLK PVFA QWVQSIHTLA PGNTTPNALA TASYAFGGDV VAVGNKVAMM PISLGTADFM VHHIHAFTIH VTVLILLKGV LFSRNS RLI PDKANLGFRF PCDGPGRGGT CQSSAWDSVF LGLFWMYNCI SVVIFHFSWK MQSDVWGTVQ ADGTVTHITG GNFAQSA IT INGWLRDFLW AQASQVIQSY GSALSAYGLI FLGAHFIWAF SLMFLFSGRG YWQELIESIV WAHNKLNVAP AIQPRALS I TQGRAVGLAH YLLGGIGTTW AFFLARIISV 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
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 82.087664 KDa
SequenceString: MATKFPKFSQ ALAQDPATRR IWYGLATAHD LESHDGMTEE NLYQKIFASH FGHLAVIFLW TSGNLFHLAW QGNFEQWVLN PLKVKPIAH AIWDPHFGQP AVKAFTKGGV SYPVNIATSG VYHWWYTIGM RSNTDLYAGS LFLLFLAGVF LFAGWLHLQP K FRPGLSWF ...String:
MATKFPKFSQ ALAQDPATRR IWYGLATAHD LESHDGMTEE NLYQKIFASH FGHLAVIFLW TSGNLFHLAW QGNFEQWVLN PLKVKPIAH AIWDPHFGQP AVKAFTKGGV SYPVNIATSG VYHWWYTIGM RSNTDLYAGS LFLLFLAGVF LFAGWLHLQP K FRPGLSWF KNNESRLNHH LSGLFGFSSL AWSAHLIHVA IPEARGQHVG WDNFTKVAPH PAGLQPFFSG NWGVYAAAPD TT NHIFGTS EGAGTAILTF LGGFHPQTQA LWLTDIAHHH LAIGVVFIFA GHMYRTNWGI GHSLKEILDA HRPPGGRLGA GHK GIFETL TNSLHFQLGL ALASLGVITS LVAQHMYALP SYAFIAKDYV TQSALYTHHQ YIAGFLMVGA FAHGAIFFVR DYDP EQNKN NVLARILDHK EAIISHLSWV SLFLGFHTLG IYVHNDVVVA FGTPEKQILV EPVFAQWIQA SSGKALYGFD VFLSS SNSV ATNASSNIWL PGWLEAINSG KNSLFLPIGP GDFLIHHAIA LALHTTTLIL VKGALDARGS KLMPDKKDFG YSFPCD GPG RGGTCDISAW DAFYLSMFWM LNTIGWVTFY WHWKHVTIWQ GNAGQFNESS TYIMGWLRDY LWLNSSPLIN GYNPFGM NS LSVWSWMFLF GHLIWATGFM FLISWRGYWQ ELIETLVWAH ERTPLANLVR WKDKPVALSI VQARLVGLIH FTAGYIFT Y AAFVIASTTG 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
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 8.759131 KDa
SequenceString:
MSHSVKVYDT CIGCTQCVRA CPCDVLEMVS WDGCKAGQIA SAPRTEDCIG CKRCETACPT DFLSVRVYLG GETTRSMGLA Y

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Macromolecule #4: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 15.585724 KDa
SequenceString:
MAETLNLQIP SPTFEGSTGG WLRAAEVEEK YAITWTSPKE QVFEMPTGGA AIMRQGENLL YLARKEQCLA LATQVKNSFK ITDYKVYRI FPSGEVQYLH PKDGVFPEKV NAGRVGVGNV SHSIGKNLNP AQIKFTSKSF NG

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 7.309363 KDa
SequenceString:
MVKRGSKVRI LRKESYWYQD IGTVATIDTS GIRYPVVVRF EKVSYSGVNT NNFSLDEVVE VVAK

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Macromolecule #6: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 20.849227 KDa
SequenceString:
MEIFFVKNWV SMLLVCSFLA FPSLAKADVA GLTPCGESKE FARRLDGSVK KLQTRLKKYE AGTPPALALQ KQIDKTKNRF DRYGKAGLL CGTDGLPHLI ADGRWSHSGE FVIPGLFFLY VAGWIGWVGR SYVLFARTAD KPTEKEIIID VPVALSFVST G FIWPFSAF KEFTSGNLIV PADEITVSPR

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Macromolecule #7: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 3.628386 KDa
SequenceString:
MTAAYLPSIL VPIIGLIFPG LVMAFAFIYI EQD

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 4.974812 KDa
SequenceString:
MDSNFLKYLS TAPVLFTVWL SFTASFIIEA NRFFPDMLYF PM

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Macromolecule #9: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 16.489076 KDa
SequenceString:
MSQFIKPYND DPFVGNLATP VSTSSFTKSL LSNLPAYRAG LSPLLRGVEI GLTHGYFLVG PFYKLGPLRN SDVALLSGFF SALGLIIIL VACLTIYGVV SFEETEAKDQ LQTAKGWRQF TSGWLVGSVG GASFAYILIS NIPFLQTAGM SMLK

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Macromolecule #10: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 3.31807 KDa
SequenceString:
MISDTQIFIA LILALVSLVL AIRLGRALYQ

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Macromolecule #11: PsaO

MacromoleculeName: PsaO / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 15.907449 KDa
SequenceString:
SSADMRTAVI FLAVLASASA FAPAAMPTQL GKPAAFTPSL RSARVAPSPL SVVAQSKFEV SDGTPYDLNV PLVGAASFIG WVVPTLLPS QIPLYGGKGL STAFFASIGT NLAKFPAPPG MTDPFWLLCF IWHSGLFATM ILGSIGYNGY AAKK

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Macromolecule #12: Photosystem I reaction center subunit PsaK

MacromoleculeName: Photosystem I reaction center subunit PsaK / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 8.628179 KDa
SequenceString:
MNADLLIALV PQTVAWSAKT GAVMVLSNIL CIVAGRYVIQ VKGTGPSLPI SGSFAGFGLP ELLASTSLGH IVGSGAILGL SYVGVL

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Macromolecule #13: ACPI-s

MacromoleculeName: ACPI-s / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 31.529 KDa
SequenceString: LTIAFSLTMR TSVLILAGVA VAQAFSPAVV STGGLTSVRM AQAPPPASGK PLPKAKINCL EVNKKQWGIE GGAAAPGSAA PPAPKKAAV KKAAAAAGGA AVGFSGVPSQ FGRPESGVYP AEPSEQTFLG MRGPRAPGHR ENFGGKHTAT MLAIAALLWQ P VSEAGMYR ...String:
LTIAFSLTMR TSVLILAGVA VAQAFSPAVV STGGLTSVRM AQAPPPASGK PLPKAKINCL EVNKKQWGIE GGAAAPGSAA PPAPKKAAV KKAAAAAGGA AVGFSGVPSQ FGRPESGVYP AEPSEQTFLG MRGPRAPGHR ENFGGKHTAT MLAIAALLWQ P VSEAGMYR MQGDGSLTKT SFNEFEVPGF GNAKKVPTIE SLFPFSSKGF DASPVLFGKN SMIVVEDPRD GCGAYANSGS CH TFLDEIG DALKASPETL PRSEGKATYS FPWMYEHVRG RSRLAVSQLG ATQSLSLWVS PVRVW

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Macromolecule #14: ACPI-c

MacromoleculeName: ACPI-c / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 23.785516 KDa
SequenceString: MLRTALIAAC VASASAFAPG FAPMAMKSRS SAVSSMRMQE GDFSAAVPFL KRPTNLDGQY IGDVGFDPLG FSDVFDLRVL REAELKHGR FAMLATLGFI VQELYTFPFF PKMAPVDAHD YFVKQGGGSQ IIFWISFVEL FGVVALFETL QGKREPGDFA F DPLGLAKD ...String:
MLRTALIAAC VASASAFAPG FAPMAMKSRS SAVSSMRMQE GDFSAAVPFL KRPTNLDGQY IGDVGFDPLG FSDVFDLRVL REAELKHGR FAMLATLGFI VQELYTFPFF PKMAPVDAHD YFVKQGGGSQ IIFWISFVEL FGVVALFETL QGKREPGDFA F DPLGLAKD EATLERYRLA EVKHARLAMI AIGGFIHQYW VTKQTVLEQL GNFKSLA

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Macromolecule #15: ACPI-a

MacromoleculeName: ACPI-a / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 23.380867 KDa
SequenceString: MMRAVLVLAT GVASASAFAP AANFAGLSTS SRAAIARGPR MQEMSEAIPF LPKPANIDAS MPGYSGFDPL GFSDYYNVKW MQEAEIKHG RICMLAALGM MFPEFGTLPQ FSSFSTNPLE AFYQVGPAGW GQILLFIGVL ESFSYEKVFY GDSAPGDLGF D PLRMSSNA ...String:
MMRAVLVLAT GVASASAFAP AANFAGLSTS SRAAIARGPR MQEMSEAIPF LPKPANIDAS MPGYSGFDPL GFSDYYNVKW MQEAEIKHG RICMLAALGM MFPEFGTLPQ FSSFSTNPLE AFYQVGPAGW GQILLFIGVL ESFSYEKVFY GDSAPGDLGF D PLRMSSNA ASAKHYARAE VMNGRLAMIG FSGMLHHAIL TKQGPITQIV EQNFVPGAR

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Macromolecule #16: ACPI-b

MacromoleculeName: ACPI-b / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 24.814875 KDa
SequenceString: MLRNVLIAAC VAGTAAFTAS PALFRAGAVT RATSGISGMQ MQAKSKAVPF LSQPEALDGS MAGDVGFDPF GFSSNFDLKW LREAELKHG RICMLAATGC LVQEVVHLPG EAFSQKMALN AWAAAPRGGM ISILVAIGLI ELISNRFALT ATDMFANPNR V PGDLGFDP ...String:
MLRNVLIAAC VAGTAAFTAS PALFRAGAVT RATSGISGMQ MQAKSKAVPF LSQPEALDGS MAGDVGFDPF GFSSNFDLKW LREAELKHG RICMLAATGC LVQEVVHLPG EAFSQKMALN AWAAAPRGGM ISILVAIGLI ELISNRFALT ATDMFANPNR V PGDLGFDP LSLGGNGANR ARMELAEITH GRAAMMGFSG MVHQMLVSKQ APIEQLMHFK AVDSSMMKLG GAAGNLGY

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Macromolecule #17: ACPI-h

MacromoleculeName: ACPI-h / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 23.646422 KDa
SequenceString: SMLRSAVALA LVAGATAFAP GAMGPGLQLR AQGAAQRAPA RAGLSSLSMA QNPMSKAVAD FAESSPEFGG RGLGVTVNAE RWNGRHAMF GIFAMVMTSY MKGHGLIPDA DKILDVAQWG SLASVWDGAG NGISNERAII LIAHVHVLVV SVIAAVAPFG F QDTLVKEK ...String:
SMLRSAVALA LVAGATAFAP GAMGPGLQLR AQGAAQRAPA RAGLSSLSMA QNPMSKAVAD FAESSPEFGG RGLGVTVNAE RWNGRHAMF GIFAMVMTSY MKGHGLIPDA DKILDVAQWG SLASVWDGAG NGISNERAII LIAHVHVLVV SVIAAVAPFG F QDTLVKEK GYTPEAPAGL IPPFKTGLTP EAELINGRLA MLGIISIVTA SVFTGTPVVD TINLGMGKIL Y

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Macromolecule #18: ACPI-m,f,j

MacromoleculeName: ACPI-m,f,j / type: protein_or_peptide / ID: 18 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 22.379064 KDa
SequenceString: TVAAVACVAS AAAFAPSAPM GVKASTRAVS KIGPRMQAMS DSVPFLKQPE ALDGSMAGDV GFDPLGFSSI GDINFLREAE LKHGRIAML AAAGSIAQDI FTFPGVSKVV GTAKMTGVHD ILVKQGAMGQ LLLWLSFLEV FGTIALLETL DGKRAPGDFK F DPLNFSKN ...String:
TVAAVACVAS AAAFAPSAPM GVKASTRAVS KIGPRMQAMS DSVPFLKQPE ALDGSMAGDV GFDPLGFSSI GDINFLREAE LKHGRIAML AAAGSIAQDI FTFPGVSKVV GTAKMTGVHD ILVKQGAMGQ LLLWLSFLEV FGTIALLETL DGKRAPGDFK F DPLNFSKN PETFKRYQLA EIKNGRLAMM GVGGMVHGYF ITGKGPLELL GNFK

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Macromolecule #19: ACPI-e

MacromoleculeName: ACPI-e / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 22.654332 KDa
SequenceString: TMFRLTLLAC VASASAFAPS ALLPSSGVRV AKTGMRMQEN LAIPFLKAPA NLDSSMPGYA GFDPLGFSDN YDIKWLQESE LKHGRVAML GVVGLLVPEF VHLPMYDAAS TPYDAYTTVP AFALTQILMG CGIHEFRTHK GKMSPDNMFD DGRAPGDFGW G KGKADAVM ...String:
TMFRLTLLAC VASASAFAPS ALLPSSGVRV AKTGMRMQEN LAIPFLKAPA NLDSSMPGYA GFDPLGFSDN YDIKWLQESE LKHGRVAML GVVGLLVPEF VHLPMYDAAS TPYDAYTTVP AFALTQILMG CGIHEFRTHK GKMSPDNMFD DGRAPGDFGW G KGKADAVM ATKEIKNGRL AMLAFGGILH QQLLTKMGTI AHLTGGFKPL EF

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Macromolecule #20: ACPI-l

MacromoleculeName: ACPI-l / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 18.985742 KDa
SequenceString:
DNAMPFLEGP PKLDGSLAGD VGFDPVGFSN YFDIRWLREA ELKHGRVCML GVTGLLVQEA ICLPQFANGK TPVDDFFVVP AAGLWQVFF TIGAVEFFSN GFKLTPGDMF SEGREAGDLG FDPLGCGKNP DALARRRLVE VKNGRLAMIA FGGMLHQQLL T GQGTLEQL ANFKAIN

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Macromolecule #21: ACPI-k

MacromoleculeName: ACPI-k / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 24.658832 KDa
SequenceString: AASAFAPAAL PSMARTTARS GVTMQLYKDG VMQGKGLVAV PFALAPDSLP ADIPGYVGFD PLGLSTLCNL DFLREAEIKH GRVAMLAVT GSLVQDVFQF PGVDKVIGNA KMIGAHDKFI AGAHAGDTRS FAMHQIIFWV GLLEVLTMPA LFETMNGGPR Q PGDFKFDP ...String:
AASAFAPAAL PSMARTTARS GVTMQLYKDG VMQGKGLVAV PFALAPDSLP ADIPGYVGFD PLGLSTLCNL DFLREAEIKH GRVAMLAVT GSLVQDVFQF PGVDKVIGNA KMIGAHDKFI AGAHAGDTRS FAMHQIIFWV GLLEVLTMPA LFETMNGGPR Q PGDFKFDP LGLGKGDKLA RKQLTEIKNG RLAMIGVGGM VHHYLLTGKG PLQFLAGIPN YKSCIDPHMG PLCQ

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Macromolecule #22: ACPI-i

MacromoleculeName: ACPI-i / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 21.402549 KDa
SequenceString: LLQGSGRTAA VSGLSGMKMQ DMSASVPFLP RPAALDGSMV GDVGFDPLGF TTKYDIKWLR EAELKHGRVC MLASLGCIVQ EFVHLPSEA TSNPVASEAF FQVPAGGLWQ IFAAIGIIEH FSNNFKMSGS TMFSDGRAPG DLSFDPLNFG KNPSARARYE L AEIKNGRL ...String:
LLQGSGRTAA VSGLSGMKMQ DMSASVPFLP RPAALDGSMV GDVGFDPLGF TTKYDIKWLR EAELKHGRVC MLASLGCIVQ EFVHLPSEA TSNPVASEAF FQVPAGGLWQ IFAAIGIIEH FSNNFKMSGS TMFSDGRAPG DLSFDPLNFG KNPSARARYE L AEIKNGRL AMMGFSGMIH GCFITGKGPL GALGSLDWHQ SF

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Macromolecule #23: ACPI-d

MacromoleculeName: ACPI-d / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 23.069039 KDa
SequenceString: LPPAMFRLSL CAAIVASASA FAPSSVLPTA TRRAGAVSAM KMQMPVAIPP LGRPETDMFD GSVPGDAGFD PLVISGWLDS RWLREAEVK HGRVAMLAAA GCIAQDLFTF PGVTQVFSPG TKMSALHDAA VKAGSMQQML WPIAILETIS IAATIQMLQG S GRAPGDFG ...String:
LPPAMFRLSL CAAIVASASA FAPSSVLPTA TRRAGAVSAM KMQMPVAIPP LGRPETDMFD GSVPGDAGFD PLVISGWLDS RWLREAEVK HGRVAMLAAA GCIAQDLFTF PGVTQVFSPG TKMSALHDAA VKAGSMQQML WPIAILETIS IAATIQMLQG S GRAPGDFG FDPLGLGKGA KAERMALCEI KNGRLAMIGF SGMMHHYFIT GKGPIELLTS R

+
Macromolecule #24: ACPI-g

MacromoleculeName: ACPI-g / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 22.954898 KDa
SequenceString: AKSKAIPFLD APPALSESMP GYVGFDPLWV SSMLPDAGYV KFLQEAEIKH GRVAMLAAAG AIVQDIFTFP GVTSVIGNVK MTSVHDTFL SMEGPGKGNQ AAMHQLLLWL GILEIATSVA IIQSFKGETN RAPGDFGFDP LGFSKKAGAE TMALKEIKNG R LAMIGIGG ...String:
AKSKAIPFLD APPALSESMP GYVGFDPLWV SSMLPDAGYV KFLQEAEIKH GRVAMLAAAG AIVQDIFTFP GVTSVIGNVK MTSVHDTFL SMEGPGKGNQ AAMHQLLLWL GILEIATSVA IIQSFKGETN RAPGDFGFDP LGFSKKAGAE TMALKEIKNG R LAMIGIGG MVHHYLLTGK GPLQFLGGIP NYKSCVSHPD SLLPWLIKPV GAVLPKIC

+
Macromolecule #25: PsaR

MacromoleculeName: PsaR / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 13.949042 KDa
SequenceString:
SFAMAALRCT VLLLAVASAS AFVSGPATLA LRSNPRAAIS RGPQMYSPVP SPEGTKEVYW ETKAPSSDVL GIGAGVSSGN FAASSVVAL MIGGFCTGQV IPLTSDPNPL FLIGSFLLPY SWALHVAAWI QKNNGK

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Macromolecule #26: ACPI-n

MacromoleculeName: ACPI-n / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 23.06983 KDa
SequenceString: LRSVAVCACL ASAAAFAPSA VLPRAATRAA ALRGPSMQLY KDGKMQGKGV NIIPVFARPD SLDGTIPGDQ GFDPFGFSSW VNMKFVSEA EIKHGRLAML AFAGIMVESI GISFPGATSI LGDSKDIFEI HNKAVESGAM GQILLWVGFI EACVGVPAMN E MLSGETSR ...String:
LRSVAVCACL ASAAAFAPSA VLPRAATRAA ALRGPSMQLY KDGKMQGKGV NIIPVFARPD SLDGTIPGDQ GFDPFGFSSW VNMKFVSEA EIKHGRLAML AFAGIMVESI GISFPGATSI LGDSKDIFEI HNKAVESGAM GQILLWVGFI EACVGVPAMN E MLSGETSR MPGDFGFDPL GLGKGDKLAR KQLVEVTNGR LAMLAVSGIV HHTIITGKGP LQ

+
Macromolecule #27: PsaQ

MacromoleculeName: PsaQ / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 23.676062 KDa
SequenceString: YVALAAASAE AFSSPALSGL KMSAEPTQIS RKDLLSTAAA GIIAVPAIAG AASLDPKTGF PVQSGGRDTL CGGSASAGCQ PMTQAASIT DKQKTVLAGK ITVAANKVPV LTAAVEKMKS GKKPKMDRDY VLRFSALYLT TLVDAMDQYC LRDANGAKAA G GAGIPKVG ...String:
YVALAAASAE AFSSPALSGL KMSAEPTQIS RKDLLSTAAA GIIAVPAIAG AASLDPKTGF PVQSGGRDTL CGGSASAGCQ PMTQAASIT DKQKTVLAGK ITVAANKVPV LTAAVEKMKS GKKPKMDRDY VLRFSALYLT TLVDAMDQYC LRDANGAKAA G GAGIPKVG GFKSTLAPSS ASALYGNVDS IKEDMQTIRD AAFKGDFDGV IKAAGDIQTS ATAFLGQANP PIVFN

+
Macromolecule #28: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 28 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #29: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 29 / Number of copies: 255 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #30: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 30 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

+
Macromolecule #31: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 31 / Number of copies: 22 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #32: 1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tet...

MacromoleculeName: 1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyl-18-[(1R)-2,6,6-trimethylcyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohexene
type: ligand / ID: 32 / Number of copies: 29 / Formula: WVN
Molecular weightTheoretical: 536.873 Da

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Macromolecule #33: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 33 / Number of copies: 5 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #34: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 34 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #35: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

MacromoleculeName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
type: ligand / ID: 35 / Number of copies: 1 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

+
Macromolecule #36: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 36 / 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 #37: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 37 / Number of copies: 9 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #38: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...

MacromoleculeName: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17- ...Name: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol
type: ligand / ID: 38 / Number of copies: 58 / Formula: II0
Molecular weightTheoretical: 564.84 Da
Chemical component information

ChemComp-II0:
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol

+
Macromolecule #39: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...

MacromoleculeName: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
type: ligand / ID: 39 / Number of copies: 12 / Formula: IHT
Molecular weightTheoretical: 550.856 Da
Chemical component information

ChemComp-IHT:
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol

+
Macromolecule #40: Chlorophyll c2

MacromoleculeName: Chlorophyll c2 / type: ligand / ID: 40 / Number of copies: 20 / Formula: KC2
Molecular weightTheoretical: 608.926 Da
Chemical component information

ChemComp-KC2:
Chlorophyll c2

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Macromolecule #41: water

MacromoleculeName: water / type: ligand / ID: 41 / Number of copies: 422 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8wm6

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38563
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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