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- EMDB-51482: Universal PSII assembly intermediate -

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Basic information

Entry
Database: EMDB / ID: EMD-51482
TitleUniversal PSII assembly intermediate
Map data
Sample
  • Complex: Photosystem II
    • Protein or peptide: x 20 types
  • Ligand: x 20 types
KeywordsGreen alga / PSII / D.salina / membrane protein / Cryo-EM / PHOTOSYNTHESIS / assembly intermediate / water-ferricyanide oxidoreductase.
Function / homology
Function and homology information


chloroplast thylakoid / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem II ...chloroplast thylakoid / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem II / response to herbicide / extrinsic component of membrane / chlorophyll binding / photosynthetic electron transport in photosystem II / : / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis, light reaction / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / calcium ion binding / metal ion binding
Similarity search - Function
PsbP, C-terminal / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide ...PsbP, C-terminal / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein J / Photosystem II reaction center protein H / Cytochrome b559 subunit beta / Uncharacterized protein / Photosystem II PsbX / Oxygen-evolving enhancer protein 2, chloroplastic / PSII 6.1 kDa protein / Photosystem II reaction center protein K ...Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein J / Photosystem II reaction center protein H / Cytochrome b559 subunit beta / Uncharacterized protein / Photosystem II PsbX / Oxygen-evolving enhancer protein 2, chloroplastic / PSII 6.1 kDa protein / Photosystem II reaction center protein K / Photosystem II reaction center protein I / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein Z / Photosystem II reaction center protein M / Cytochrome b559 subunit alpha / Photosystem II reaction center protein T / Photosystem II protein D1 / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein L
Similarity search - Component
Biological speciesDunaliella salina (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsFadeeva M / Klaiman D / Nelson N
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation199/21 Israel
CitationJournal: To Be Published
Title: Universal PSII assembly intermediate
Authors: Fadeeva M / Klaiman D / Nelson N
History
DepositionSep 4, 2024-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51482.png

Downloads & links

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Map

FileDownload / File: emd_51482.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 300 pix.
= 193.5 Å		0.65 Å/pix.
x 300 pix.
= 193.5 Å		0.65 Å/pix.
x 300 pix.
= 193.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.645 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0047
Minimum - Maximum-0.018178247 - 0.027882786
Average (Standard dev.)0.000059366386 (±0.0016631682)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 193.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51482_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51482_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Photosystem II

EntireName: Photosystem II
Components
  • Complex: Photosystem II
    • Protein or peptide: Photosystem II protein D1
    • Protein or peptide: Photosystem II CP47 reaction center protein
    • Protein or peptide: Photosystem II reaction center protein Psb30
    • 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 J
    • Protein or peptide: Photosystem II reaction center protein K
    • Protein or peptide: Photosystem II reaction center protein L
    • Protein or peptide: Photosystem II reaction center protein M
    • Protein or peptide: PsbO
    • Protein or peptide: PsbP
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: PSII 6.1 kDa protein
    • Protein or peptide: Photosystem II PsbX
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: Photosystem II reaction center protein U, PsbU
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: FE (II) ION
  • Ligand: CHLORIDE ION
  • Ligand: CHLOROPHYLL A
  • Ligand: PHEOPHYTIN A
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: SODIUM ION
  • Ligand: BICARBONATE ION
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: DIACYL GLYCEROL
  • 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: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (3R)-beta,beta-caroten-3-ol
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: water

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Supramolecule #1: Photosystem II

SupramoleculeName: Photosystem II / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 37.291488 KDa
SequenceString: ENTSLWARFC EWITSTENRL YIGWFGVIMI PTLLTAISVY IIAFIAAPPV DIDGIREPVS GSLLYGNNII TGAVVPTSNA IGLHFYPIW EAASLDEWLY NGGPYQLVVC HFFLGVCCYM GREWELSYRL GMRPWIAVAY SAPVAAATAV FIIYPIGQGS F SDGMPLGI ...String:
ENTSLWARFC EWITSTENRL YIGWFGVIMI PTLLTAISVY IIAFIAAPPV DIDGIREPVS GSLLYGNNII TGAVVPTSNA IGLHFYPIW EAASLDEWLY NGGPYQLVVC HFFLGVCCYM GREWELSYRL GMRPWIAVAY SAPVAAATAV FIIYPIGQGS F SDGMPLGI SGTFNFMIVF QAEHNILMHP FHMFGVAGVF GGSLFSAMHG SLVTSSLIRE TTENESANAG YKFGQEEETY NI VAAHGYF GRLIFQYASF NNSRSLHFFL AVWPVVCIWL TALGISTMAF NLNGFNFNQS VVDSNGRVLN TWADIINRAN LGM EVMHER NAHNFPLDLA

UniProtKB: Photosystem II protein D1

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 53.321516 KDa
SequenceString: GLPWYRVHTV VINDPGRLIS VHLMHTALVA GWAGAMTLFE IAVFDPSDPV LNPMWRQGMF VLPFLTRLGV TQSWGGWTIS GETSSNPGI WSYEGAAASH IVLSGLLFLA SVWHWVYWDL ELFRDPRTGK TALDLPKIFG IHLFLAGLLC FGFGAFHVTG V FGPGIWVS ...String:
GLPWYRVHTV VINDPGRLIS VHLMHTALVA GWAGAMTLFE IAVFDPSDPV LNPMWRQGMF VLPFLTRLGV TQSWGGWTIS GETSSNPGI WSYEGAAASH IVLSGLLFLA SVWHWVYWDL ELFRDPRTGK TALDLPKIFG IHLFLAGLLC FGFGAFHVTG V FGPGIWVS DPYGLTGSVQ PVAPSWGAEG FDPYNPGGVP AHHIAAGILG VLAGLFHL(CSD)V RPSIRLYFGL SMGSIESV L SSSIAAVFWA AFVVAGTMWY GSAATPIELF GPTRYQWDQG FFQQEIQKRV AQSTSEGLSV SEAWAKIPEK LAFYDYIGN NPAKGGLFRT GAMNSGDGIA VGWLGHASFK DQEGRELFVR RMPTFFETFP VVLIDKDGVV RADVPFRKAE SKYSIEQVGV SVTFYGGEL NGLTFTDPST VKKYARKAQL GEIFEFDRST LQSDGVFRSS PRGWFTFGHL SFALLFFFGH IWHGSRTIFR D VFAGIDED

UniProtKB: Photosystem II CP47 reaction center protein

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Macromolecule #3: Photosystem II reaction center protein Psb30

MacromoleculeName: Photosystem II reaction center protein Psb30 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 3.349144 KDa
SequenceString:
MSLTLILQLV ALFAVVAAGP LVVVLLSVRG GNL

UniProtKB: Photosystem II reaction center protein Psb30

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Macromolecule #4: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 49.128992 KDa
SequenceString: GRDQETTGFA WWAGNARLIN LSGKLLGAHV AHAGLIVFWA GAMNLFEVSH FVPEKPMYEQ GLILLPHIAT LGYGVGPGGE VLDTFPYFV SGVLHLISSA VLGFGGVYHS LIGPETLEES YPFFGYVWKD KNKMTNILGY HLIILGCGAW LLVLKALYFG G VYDTWAPG ...String:
GRDQETTGFA WWAGNARLIN LSGKLLGAHV AHAGLIVFWA GAMNLFEVSH FVPEKPMYEQ GLILLPHIAT LGYGVGPGGE VLDTFPYFV SGVLHLISSA VLGFGGVYHS LIGPETLEES YPFFGYVWKD KNKMTNILGY HLIILGCGAW LLVLKALYFG G VYDTWAPG GGDVRIISNP TTNAAIIFGY IVKSPFGGDG WIVSVDNLED IIGGHIWIGT LCILGGIWHI YTTPWPWARR AF VWSGEAY LSYSLAAVSL MGFTACCFAW FNNTAYPSEF YGPTGPEASQ AQAFTFLVRD QRLGANVASA QGPTGLGKYL MRS PTGEII FGGETMRFWD FRGPWVEPLR GPSGLDLVKL KNDIQPWQER RAAEYMTHAP LGSLNSVGGV ATEINAVNFV SPRS WLATS HFCLGFFFFV GHLWHAGRAR AAAAGFEKGI DRVDEPVLSM RPLD

UniProtKB: Photosystem II CP43 reaction center protein

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Macromolecule #5: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 38.965383 KDa
SequenceString: IGTYQEKRTW FDDADDWLRQ DRFVFVGWSG LLLLPCAYFA VGGWLTGCTF VTSWYTHGLA SSYIEGCNFL TAAVSTPANS LGHSLLFVW GPEAQGDLTR WFQLGGLWAF VALHGAFGLI GFMLRQFEIA RSVNLRPYNA IAFSAPIAVF VSVFLIYPLG Q SGWFFAPS ...String:
IGTYQEKRTW FDDADDWLRQ DRFVFVGWSG LLLLPCAYFA VGGWLTGCTF VTSWYTHGLA SSYIEGCNFL TAAVSTPANS LGHSLLFVW GPEAQGDLTR WFQLGGLWAF VALHGAFGLI GFMLRQFEIA RSVNLRPYNA IAFSAPIAVF VSVFLIYPLG Q SGWFFAPS FGVASIFRFI LFFQGFHNWT LNPFHMMGVA GVLGAALLCA IHGATVENTL FEDGDGANTF RAFNPTQAEE TY SMVTANR FWSQIFGVAF SNKRWLHFFM LFVPVTGLWM SALGVVGLAL NLRAYDFVSQ EIRAAEDPEF ETFYTKNILL NEG IRAWMA AQDQPHEKLT LPEEVLPRGN AL

UniProtKB: Photosystem II D2 protein

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Macromolecule #6: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 8.743847 KDa
SequenceString:
ERPFSDILTS IRYWVIHSIT VPSLFIAGWL FVSTGLAYDV FGSPRPNEYF TEDRQDAPLI TDRFNALEQV KKLSAQ

UniProtKB: Cytochrome b559 subunit alpha

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Macromolecule #7: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 3.549299 KDa
SequenceString:
IFTVRWLAIH AIAVPTIFFL GAITAMQFIQ R

UniProtKB: Cytochrome b559 subunit beta

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Macromolecule #8: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 7.124381 KDa
SequenceString:
EPGIVTPLGT LLRPLNSEAG KVLPGWGTTV LMAVAILLFA VFLLIILEIY NSSLILDGVT NSWESLA

UniProtKB: Photosystem II reaction center protein H

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Macromolecule #9: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 3.743417 KDa
SequenceString:
MLTLKIFVYT VVTFFVGLFI FGFLSNDPSR NPG

UniProtKB: Photosystem II reaction center protein I

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Macromolecule #10: Photosystem II reaction center protein J

MacromoleculeName: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 3.725447 KDa
SequenceString:
TGRIPLWLVG TVVGLLAIGL LAIFFYGSYV GLGSSL

UniProtKB: Photosystem II reaction center protein J

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Macromolecule #11: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 4.159991 KDa
SequenceString:
KLPEAYAPFS PIVDVLPIIP VLFILLAFVW QASVSFR

UniProtKB: Photosystem II reaction center protein K

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Macromolecule #12: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 4.214929 KDa
SequenceString:
RPNPNKQVVE LNRSSLYWGL LLIFVLAVLF SSYIFN

UniProtKB: Photosystem II reaction center protein L

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Macromolecule #13: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 3.320033 KDa
SequenceString:
VNILGLIATA LFIIIPTSFL LILYVKTAAS E

UniProtKB: Photosystem II reaction center protein M

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Macromolecule #14: PsbO

MacromoleculeName: PsbO / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 25.874908 KDa
SequenceString: LTYDELQGLT YLQVKGTGIA NTCPVVEQGT SNVRELKPGD YKLEKFCMEP TSFTVKEEDA KGREEFVKTK LLTRLTYGLD GMNGSMKIN NDGSVEFRED EGLDYAATTV KLPGGEYVPF LFTIKEFDGK GTLDSFSGDF LVPSYRGSTF LDPKGRGGAT G YDNAIALP ...String:
LTYDELQGLT YLQVKGTGIA NTCPVVEQGT SNVRELKPGD YKLEKFCMEP TSFTVKEEDA KGREEFVKTK LLTRLTYGLD GMNGSMKIN NDGSVEFRED EGLDYAATTV KLPGGEYVPF LFTIKEFDGK GTLDSFSGDF LVPSYRGSTF LDPKGRGGAT G YDNAIALP AKADADEIQR LNNKSYTPGK GSAVFSVAKV DTETGEIAGV FESIQPSDTE MGAHPAKDIK ITGLWYGQLT

UniProtKB: Uncharacterized protein

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Macromolecule #15: PsbP

MacromoleculeName: PsbP / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 20.553898 KDa
SequenceString:
AYGEGANVFG RVTNKSGFVP YAGDSFALLL PSKWNPSDQK EVESIVLRYE DNFDAVNNLY VVEDKSDKSS IEAYGTPEEF ISQFGYLLG KQAWAGQTVS EGGFDANRVS NAALLGVATE KDKKGKTYYK FEILTRTADG NEGGRHQLVK ATVSNGKLYL L KVQAGDKR WFKGTDKECL GVLDSFTVV

UniProtKB: Oxygen-evolving enhancer protein 2, chloroplastic

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Macromolecule #16: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 3.478194 KDa
SequenceString:
MEALVYTFLL IGTLGIIFFS IFFREPPRIA

UniProtKB: Photosystem II reaction center protein T

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Macromolecule #17: PSII 6.1 kDa protein

MacromoleculeName: PSII 6.1 kDa protein / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 4.755367 KDa
SequenceString:
LVDDRMNGDG TGLPFGVNDG ILGWVIAGTL GTIWAIYFVS QKDLG

UniProtKB: PSII 6.1 kDa protein

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Macromolecule #18: Photosystem II PsbX

MacromoleculeName: Photosystem II PsbX / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 3.202762 KDa
SequenceString:
SVTPSLKNFL LSLVAGAVVL AAIAGAVTAV SNF

UniProtKB: Photosystem II PsbX

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Macromolecule #19: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 6.430616 KDa
SequenceString:
MTSILQIALL GLVLVSFALV VGVPVVFASP NGWTENKGVV FSGLSVWFLL VFAVGVFNSF A

UniProtKB: Photosystem II reaction center protein Z

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Macromolecule #20: Photosystem II reaction center protein U, PsbU

MacromoleculeName: Photosystem II reaction center protein U, PsbU / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant) / Organ: chloroplast
Molecular weightTheoretical: 3.377869 KDa
SequenceString:
RVRTVLDMDR KDPAKEETVK ELRKDINN

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Macromolecule #21: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 21 / Number of copies: 1 / Formula: OEX
Molecular weightTheoretical: 339.827 Da
Chemical component information

ChemComp-OEX:
CA-MN4-O5 CLUSTER

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Macromolecule #22: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 22 / Number of copies: 1 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #23: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 23 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #24: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 24 / Number of copies: 35 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #25: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 25 / Number of copies: 2 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #26: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 26 / Number of copies: 8 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #27: 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: 27 / Number of copies: 2 / 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 #28: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 28 / Number of copies: 8 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #29: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 29 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Macromolecule #30: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 30 / Number of copies: 1 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION

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

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 31 / Number of copies: 5 / 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~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},...

MacromoleculeName: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca- ...Name: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
type: ligand / ID: 32 / Number of copies: 1 / Formula: C7Z
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-C7Z:
(1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol

+
Macromolecule #33: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 33 / 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 #34: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 34 / Number of copies: 1 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

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Macromolecule #35: DIACYL GLYCEROL

MacromoleculeName: DIACYL GLYCEROL / type: ligand / ID: 35 / Number of copies: 1 / Formula: DGA
Molecular weightTheoretical: 625.018 Da
Chemical component information

ChemComp-DGA:
DIACYL GLYCEROL

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Macromolecule #36: 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: 36 / Number of copies: 1 / 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 #37: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 37 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #38: (3R)-beta,beta-caroten-3-ol

MacromoleculeName: (3R)-beta,beta-caroten-3-ol / type: ligand / ID: 38 / Number of copies: 1 / Formula: RRX
Molecular weightTheoretical: 552.872 Da
Chemical component information

ChemComp-RRX:
(3R)-beta,beta-caroten-3-ol

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Macromolecule #39: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 39 / Number of copies: 1 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #40: water

MacromoleculeName: water / type: ligand / ID: 40 / Number of copies: 11 / 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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 29916 / 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: 2.25 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5349698
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7pi0

Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.0) / Number images used: 118340
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 4.0.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 4.0.0)
Final 3D classificationNumber classes: 2 / Avg.num./class: 60000 / Software - Name: RELION (ver. 4.0.0)
FSC plot (resolution estimation)

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