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- EMDB-62846: cryo-EM structure of PSII-ACPII from Rhodomonas sp. NIES-2332 -

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Basic information

Entry
Database: EMDB / ID: EMD-62846
Titlecryo-EM structure of PSII-ACPII from Rhodomonas sp. NIES-2332
Map data
Sample
  • Complex: cryo-EM structure of PSII-ACPII from Rhodomonas sp. NIES-2332
    • Protein or peptide: x 21 types
  • Protein or peptide: x 3 types
  • Ligand: x 17 types
Keywordsphotosynthesis complex / PHOTOSYNTHESIS
Function / homologyPhotosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / photosystem II / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis / protein stabilization / Photosystem II reaction center protein H
Function and homology information
Biological speciesRhodomonas sp. NIES-2332 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.17 Å
AuthorsYonehara N / 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 23, 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_62846.png

Downloads & links

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Map

FileDownload / File: emd_62846.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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.11587708 - 0.303005
Average (Standard dev.)0.00010152556 (±0.007810836)
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_62846_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_62846_half_map_2.map
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Sample components

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Entire : cryo-EM structure of PSII-ACPII from Rhodomonas sp. NIES-2332

EntireName: cryo-EM structure of PSII-ACPII from Rhodomonas sp. NIES-2332
Components
  • Complex: cryo-EM structure of PSII-ACPII from Rhodomonas sp. NIES-2332
    • Protein or peptide: Photosystem II protein D1
    • Protein or peptide: Photosystem II CP47 reaction center protein
    • Protein or peptide: Photosystem II CP43 reaction center protein
    • Protein or peptide: Photosystem II D2 protein
    • Protein or peptide: Cytochrome b559 subunit alpha
    • Protein or peptide: Cytochrome b559 subunit beta
    • Protein or peptide: Photosystem II reaction center protein H
    • Protein or peptide: Photosystem II reaction center protein I
    • Protein or peptide: Photosystem II reaction center protein K
    • Protein or peptide: Photosystem II reaction center protein L
    • Protein or peptide: Photosystem II protein M
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: Photosystem II protein W
    • Protein or peptide: Photosystem II reaction center X protein
    • Protein or peptide: Photosystem II reaction center protein Psb30
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: ACPII-2
    • Protein or peptide: ACPII-3
    • Protein or peptide: ACPII-4
    • Protein or peptide: ACPII-5
    • Protein or peptide: ACPII-6
  • Protein or peptide: ACPII-1
  • Protein or peptide: Psb-gama_linker
  • Protein or peptide: Psb-gama_linker
  • Ligand: FE (II) ION
  • Ligand: CHLOROPHYLL A
  • Ligand: PHEOPHYTIN A
  • 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: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: CHLORIDE ION
  • Ligand: MANGANESE (II) ION
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: BICARBONATE ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: Chlorophyll c2
  • 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: water

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Supramolecule #1: cryo-EM structure of PSII-ACPII from Rhodomonas sp. NIES-2332

SupramoleculeName: cryo-EM structure of PSII-ACPII from Rhodomonas sp. NIES-2332
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16, #18-#22
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)

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Macromolecule #1: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 41.541246 KDa
SequenceString: TSTIVAWEVI YYNLYKNKKM TATLERRESA SLWERFCSWI TSTENRLYIG WFGVLMIPTL LTATTVYIIA FIAAPPVDID GIREPVAGS LLYGNNIISG AVIPSSASIG IHFYPIWEAA SLDEWLYNGG PYQLIVDHFL LGVCGWIGRE WEFSYRLGMR P WISVAFTA ...String:
TSTIVAWEVI YYNLYKNKKM TATLERRESA SLWERFCSWI TSTENRLYIG WFGVLMIPTL LTATTVYIIA FIAAPPVDID GIREPVAGS LLYGNNIISG AVIPSSASIG IHFYPIWEAA SLDEWLYNGG PYQLIVDHFL LGVCGWIGRE WEFSYRLGMR P WISVAFTA PVAAASAVFL VYPIGQGSFS DGMPLGISGT FNFMLVFQAE HNILMHPFHQ LGVAGVFGGS LFSAMHGSLV TS SLIRETT ENESANYGYK FGQEEETYNI VAAHGYFGRL IFQYASFNNS RALHFFLGLW PVVGIWFTAL GIMTMAFNLN GFN FNQSVV DSQGRVINTW ADILNRANLG MEVMHERNAH NFPLDLAAGE SLPVALTA

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Macromolecule #2: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 56.199855 KDa
SequenceString: GLPWYRVHTV VLNDPGRLIA VHLMHTALVA GWAGSMALYE LAVFDPSDPV LNPMWRQGMF VMPFMARIGV TDSWGGWSIT GESVANPGF WSFEGVALAH IGLSGLLFLA AVWHWVYWDL ELFRDPRTGN PALDLPKIFG IHLLLSGVLC FGFGAFHVTG A WGPGIWVS ...String:
GLPWYRVHTV VLNDPGRLIA VHLMHTALVA GWAGSMALYE LAVFDPSDPV LNPMWRQGMF VMPFMARIGV TDSWGGWSIT GESVANPGF WSFEGVALAH IGLSGLLFLA AVWHWVYWDL ELFRDPRTGN PALDLPKIFG IHLLLSGVLC FGFGAFHVTG A WGPGIWVS DAYGITGKVQ PVAPAWGPEG FNPFNPSGVA SHHIAAGILG FAAGIFHIAV RPPQRLYRAL RMGNIETVLS SS IAAVFWS AFITTGTMWY GSATTPIELF GPTRYQWDSG YFQQEIERRV ENSLNEGLSL SEAWSRIPDK LAFYDYVGNN PAK GGLFRA GPMNKGDGIA EAWLGHPIFQ DKEGRELTVR RMPAFFETFP VILVDKDGII RADIPFRRAE SKYSIEQVGV TTSF YGGKL NGQVFTDAPT VKKYARKAQL GEVMEFDRTT LESDGVFRSS PRGWYTFGHA NFALLFFLGH LWHGSRTLFR DVFSG IGAE VTEQVEFGAF QKLGDRSTKK QGAV

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Macromolecule #3: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 53.468285 KDa
SequenceString: MKVFALGWLL KISLMKTLYS LRRFYHVETP FNSNIGIAGR DIESTGFAWW SGNSRLINVS GKLLGAHVAH AGLMVFWCGA MTLFEVAHY IPEKPLYEQG LILLPHLASL GWGVGPGGEI VDIYPYFVVG ILHIISSAVL GFGGVYHSLI GPDTLEESFP A FGYDWRDK ...String:
MKVFALGWLL KISLMKTLYS LRRFYHVETP FNSNIGIAGR DIESTGFAWW SGNSRLINVS GKLLGAHVAH AGLMVFWCGA MTLFEVAHY IPEKPLYEQG LILLPHLASL GWGVGPGGEI VDIYPYFVVG ILHIISSAVL GFGGVYHSLI GPDTLEESFP A FGYDWRDK NKITTILGIH LVILGFGALL LVVKAMYLGG LYDTWAPGGG DVRIIDNPTL NPAVIIGYVL KSPWGGDGWI CS VNNMEDI VGGHIWIGFT CIAGGFWHIL TKPFAWARRA YVWSGEAYLS YSLVAVSLMG FIASQYSWYN NTAYPSEFYG PTG PEASQS QAFTFLVRDQ RLGASVASAQ GPTGLGKYLM RSPSGEIILG GETQRFWDLR APWIEPLRGP NGLDLNKIKN DIQP WQERR AAEYMTHAPL GSLNSVGGVA TEINSVNFVS PRSWLTCAHF LLGFVFYIGH LWHAGRARAA AAGFEKGINR ENEPV LSLR PI

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Macromolecule #4: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 39.160707 KDa
SequenceString: MTIAIGQEEG RGWFDLADDW LKRDRFVFVG WSGLLLFPTS YLSIGGWFTG TTFVTSWYTH GLASSYLEGC NFFTAAVSTP ANSMGHSLL LLWGPEAQGD FTRWCQIGGL WAFCALHGSF GLIGFCLRQF EIARLVGIRP YNAIAFSGPI AIFVSVFLMY P LGQASWFF ...String:
MTIAIGQEEG RGWFDLADDW LKRDRFVFVG WSGLLLFPTS YLSIGGWFTG TTFVTSWYTH GLASSYLEGC NFFTAAVSTP ANSMGHSLL LLWGPEAQGD FTRWCQIGGL WAFCALHGSF GLIGFCLRQF EIARLVGIRP YNAIAFSGPI AIFVSVFLMY P LGQASWFF APSLGVAAIF RFLLFIQGFH NFTLNPFHMM GVAGILGAAL LCAIHGATVQ NTIFEDGDAA NTFRAFTPTQ AE ETYSMVT ANRFWSQIFG VAFSNKRWLH FFMLFVPLAG LWTSAIGIVG LALNLRAYDF VSQELRAAED PEFETFYTKN ILL NEGIRS WMAAQDQPHE NFIFPEEVLP RGNAL

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Macromolecule #5: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 9.50372 KDa
SequenceString:
MSGGSTGERP FSDIITSIRY WIIHSITIPA LFVAGWLFVS TGLAYDIFGT PRPNEYFTQE RQQVPLVNDR FSAKQELEDL TKGL

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Macromolecule #6: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 4.860847 KDa
SequenceString:
MSKIKQPISY PIFTFRWLAI HGLAVPTVFF LGAITSMQFI QR

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Macromolecule #7: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 7.429764 KDa
SequenceString:
MALRTRLGEL LRPLNSEYGK VAPGWGTTPI MGFVMLLFAV FLLIILQIYN SSLIIENVDV DWASLGS

UniProtKB: Photosystem II reaction center protein H

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Macromolecule #8: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 4.390065 KDa
SequenceString:
MFTLKIVVYT TVTLFVSLFT FGFLSNDASR NPNRKDLE

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Macromolecule #9: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 5.025104 KDa
SequenceString:
MEGIFLLAKL PEAYAVFKPI IDVAPVIPVF FLLLAFVWQA AVGFR

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Macromolecule #10: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 4.363087 KDa
SequenceString:
MSGPNPNKQP VELNRTSLFW GLLLIFVLAV LFSSYFFN

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Macromolecule #11: Photosystem II protein M

MacromoleculeName: Photosystem II protein M / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 11.85181 KDa
SequenceString:
TPFAMHASSA ALLVLACAAG AAAFAPSTPA LTGLKTTAFC QGPKLSAACR TPRAAKATAP SMSLMETANQ AVLLAEGGMN VSVAAYLAV LLGTFVPVVF LITLFIQSEA RKAAESGTE

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Macromolecule #12: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 3.7085 KDa
SequenceString:
METLVYTFLL IGTLGVLFFA VFFRDPPRIA KK

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Macromolecule #13: Photosystem II protein W

MacromoleculeName: Photosystem II protein W / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 12.592551 KDa
SequenceString:
DLIMLRTAVL CALIATAAAF SAAPMSGLQL RSGKTAMTMK SEGPMAAMNA NVAKALAPAV AAFSVAAPAF AEGTGEALGV DDGRLLVPL VLIPVFVALL YGNFASTQDN EDFFDTYDQR RK

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Macromolecule #14: Photosystem II reaction center X protein

MacromoleculeName: Photosystem II reaction center X protein / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 4.192965 KDa
SequenceString:
MTPSFSAFIN SLLAGLFIVI IPIGTALLIV SQSDRLTRN

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Macromolecule #15: Photosystem II reaction center protein Psb30

MacromoleculeName: Photosystem II reaction center protein Psb30 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 3.662478 KDa
SequenceString:
MPNLQTVAQL ISLFLILTSG PAIIVLIALR RGNL

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Macromolecule #16: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 6.656092 KDa
SequenceString:
MVAILQLLVS MLILLSFALV VSVPVILVSP GEWEKSKGLV YTGAGLWFGL VIMTAAFNSF VI

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Macromolecule #17: ACPII-1

MacromoleculeName: ACPII-1 / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 25.355334 KDa
SequenceString: MLRSAVLATV AVSASAFTSP ALFTRTSTRP AVSTAPTMQL YREGVLQGLG TDAIPGTDRP KNLDGALVGD VGFDPLGFSN WLDLRWARE AEIKHGRVAM LAATGMIVQD VYKFPGVQKT FGDASMMKLH NVAVDQGAMQ QLFLWITVLE TLTGIPAIIQ T LNGSERQP ...String:
MLRSAVLATV AVSASAFTSP ALFTRTSTRP AVSTAPTMQL YREGVLQGLG TDAIPGTDRP KNLDGALVGD VGFDPLGFSN WLDLRWARE AEIKHGRVAM LAATGMIVQD VYKFPGVQKT FGDASMMKLH NVAVDQGAMQ QLFLWITVLE TLTGIPAIIQ T LNGSERQP GDFGFDPLGC GRNPETLARR QLVELKNGRL AMIAVGGMVH HYLLVGRGPI EFVKNIPNFK NPLPPF

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Macromolecule #18: ACPII-2

MacromoleculeName: ACPII-2 / type: protein_or_peptide / ID: 18 / Number of copies: 2 / 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 #19: ACPII-3

MacromoleculeName: ACPII-3 / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 19.90092 KDa
SequenceString:
DRSYSMPFLE RPPALDGSLA GDVGFDPLGF SNYFDLKWLR EAELKHGRVC MLGCTGFITQ EKIQLPLPGF DNKVATEAFF SVPAGGLWQ IFFTLGAIEI LSNGGKLAPG DMFADGRAPG DLGFDPLNLS GDDAALRRFI LAELKHCRLA MIGLGGMLHQ M LITKQGPL DQLANFQPIQ YYGL

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Macromolecule #20: ACPII-4

MacromoleculeName: ACPII-4 / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 21.802332 KDa
SequenceString: LPRTANRAAA KTSPTMQLYK EGVLQGITVN AIPKSERPFG LDGTYVGDVG FDPLGFSSII DMRWLREAEL KHGRVCMLAA TGMIVQDVY QFPGVTKSFG DAKMTTLHDV AVKQGSMQQL LVWLGLLEIF GFVAIVQMLQ GSDRQPGDFG FDPLNCAANP D TLARRQLV ...String:
LPRTANRAAA KTSPTMQLYK EGVLQGITVN AIPKSERPFG LDGTYVGDVG FDPLGFSSII DMRWLREAEL KHGRVCMLAA TGMIVQDVY QFPGVTKSFG DAKMTTLHDV AVKQGSMQQL LVWLGLLEIF GFVAIVQMLQ GSDRQPGDFG FDPLNCAANP D TLARRQLV ELKNGRLAMI ATAGMLHHFF ITGKGPIQLI TG

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Macromolecule #21: ACPII-5

MacromoleculeName: ACPII-5 / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 24.844621 KDa
SequenceString: MFRTTLALAA VAGAAAFAPA PAFAPKASIR AATNTAPRMA VFQGDFSESV PFLKTPTNLD GSLPGDVGFD PLGFSEVFDI RVLREAELK HGRIAMLATL GYLVQEAYVF PFFDKVPPIQ AHDVLVKSGG MSQILLWTSF LEIFGGIALF QTIQGRRYPG D FAFDPLGL ...String:
MFRTTLALAA VAGAAAFAPA PAFAPKASIR AATNTAPRMA VFQGDFSESV PFLKTPTNLD GSLPGDVGFD PLGFSEVFDI RVLREAELK HGRIAMLATL GYLVQEAYVF PFFDKVPPIQ AHDVLVKSGG MSQILLWTSF LEIFGGIALF QTIQGRRYPG D FAFDPLGL SQGKNAEKLE RYQLAEIKHS RLAMLAFSGF VHQGFITKQG VLEQLGNFKP IPGFPEATFF

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Macromolecule #22: ACPII-6

MacromoleculeName: ACPII-6 / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 18.970797 KDa
SequenceString:
NAMPFLERPP KLDGSLAGDV GFDPVGFSNY FDIRWLREAE LKHGRVCMLG VTGLLVQEAI CLPQFANGKT PVDDFFVVPA AGLWQVFFT IGAVEFFSNG FKLTPGDMFS EGREAGDLGF DPLGCGKNPD ALARRRLVEV KNGRLAMIAF GGMLHQQLLT G QGTLEQLA NFKAIN

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Macromolecule #23: Psb-gama_linker

MacromoleculeName: Psb-gama_linker / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 31.784143 KDa
SequenceString: LTTRIMARTV AVLACSLLLF APSSHAFAPA GVARVGMPLR SNAVSARSAR VTPAKMAMDP SQISHIADGA QTFLSTLDTV PFIDEVTGE AQGFTAPKNH FASVIGLWVL FALPVWSAAY KQAGASNPEW FGVSQVSEDA PGIGLLAKAA PEYNGPSFRE G LEYVFSFV ...String:
LTTRIMARTV AVLACSLLLF APSSHAFAPA GVARVGMPLR SNAVSARSAR VTPAKMAMDP SQISHIADGA QTFLSTLDTV PFIDEVTGE AQGFTAPKNH FASVIGLWVL FALPVWSAAY KQAGASNPEW FGVSQVSEDA PGIGLLAKAA PEYNGPSFRE G LEYVFSFV WKPPILIAWK PRTVYDRDAM DPARDTVVSK LYKGLGGALD KTAVYDEEDQ LLILSDLVTF EETDLGRRRE KI AEQAGWY TGNPSFGRSL IEYSEQTRKG KKDMGTVTIS TEELAKLRAE AAKKE

+
Macromolecule #24: Psb-gama_linker

MacromoleculeName: Psb-gama_linker / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Molecular weightTheoretical: 31.815221 KDa
SequenceString: LTTRIMARTV AVLACSLLLF APSSHAFAPA GVARVGMPLR SNAVSARSAR VTPAKMAMDP SQISHIADGA QTFLSTLDTV PFIDEVTGE PQGFTSPKNH FASVIGLWVL FALPVWSAAY KQAGCTTPDW FGVSQVAEDA PGVGLLAKAA PEYNGPSFRE G LEYVFSFV ...String:
LTTRIMARTV AVLACSLLLF APSSHAFAPA GVARVGMPLR SNAVSARSAR VTPAKMAMDP SQISHIADGA QTFLSTLDTV PFIDEVTGE PQGFTSPKNH FASVIGLWVL FALPVWSAAY KQAGCTTPDW FGVSQVAEDA PGVGLLAKAA PEYNGPSFRE G LEYVFSFV WKPPILIAWK PRTVYDRDAM DPARDTVVSK LYKGLGGALD KTAVYDEEDQ LLILSDLVTF EETDLGRRRE KI AEQAGWY TGNPSFGRSL IEYSEQTRKG KKDMGTVTIS TEELAKLRAE AAKKE

+
Macromolecule #25: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 25 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #26: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 26 / Number of copies: 194 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #27: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 27 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #28: 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: 28 / Number of copies: 24 / Formula: WVN
Molecular weightTheoretical: 536.873 Da

+
Macromolecule #29: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...

MacromoleculeName: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
type: ligand / ID: 29 / Number of copies: 4 / Formula: PL9
Molecular weightTheoretical: 749.201 Da
Chemical component information

ChemComp-PL9:
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE

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Macromolecule #30: 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: 30 / Number of copies: 4 / 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

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Macromolecule #31: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 31 / Number of copies: 3 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #32: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 32 / Number of copies: 4 / Formula: MN
Molecular weightTheoretical: 54.938 Da

+
Macromolecule #33: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 33 / Number of copies: 22 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #34: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 34 / Number of copies: 18 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #35: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 35 / Number of copies: 4 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #36: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 36 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION

+
Macromolecule #37: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 37 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

+
Macromolecule #38: Chlorophyll c2

MacromoleculeName: Chlorophyll c2 / type: ligand / ID: 38 / Number of copies: 22 / Formula: KC2
Molecular weightTheoretical: 608.926 Da
Chemical component information

ChemComp-KC2:
Chlorophyll c2

+
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})-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: 39 / Number of copies: 46 / 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 #40: (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: 40 / Number of copies: 8 / 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

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Macromolecule #41: water

MacromoleculeName: water / type: ligand / ID: 41 / Number of copies: 676 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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:

8xlp

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28657
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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