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- EMDB-63018: Coordinates of Cryo-EM structure of the Arabidopsis thaliana C2S2... -

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Basic information

Entry
Database: EMDB / ID: EMD-63018
TitleCoordinates of Cryo-EM structure of the Arabidopsis thaliana C2S2M2-type PSII supercomplex
Map data
Sample
  • Complex: Cryo-EM structure of the Arabidopsis thaliana photosystem II(PSII-LHCII-ST2)
    • Protein or peptide: x 22 types
  • Ligand: x 16 types
Keywordsphotosystem / PLANT PROTEIN / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem II / photosystem II antenna complex / PSII associated light-harvesting complex II / nonphotochemical quenching / chloroplast stromal thylakoid / plastoglobule / response to high light intensity / thylakoid membrane / regulation of stomatal movement / chloroplast thylakoid ...photosynthesis, light harvesting in photosystem II / photosystem II antenna complex / PSII associated light-harvesting complex II / nonphotochemical quenching / chloroplast stromal thylakoid / plastoglobule / response to high light intensity / thylakoid membrane / regulation of stomatal movement / chloroplast thylakoid / thylakoid / vacuolar transport / photosynthesis, light harvesting / photosystem II oxygen evolving complex / response to abscisic acid / 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 I / photosystem II / response to herbicide / plastid / chlorophyll binding / photosynthetic electron transport in photosystem II / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis, light reaction / : / photosynthesis / chloroplast / electron transfer activity / protein stabilization / iron ion binding / protein domain specific binding / mRNA binding / heme binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Photosystem II 5kDa protein, chloroplastic / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Snf7 family / Snf7 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily ...Photosystem II 5kDa protein, chloroplastic / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Snf7 family / Snf7 / 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 / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / (thale cress) hypothetical protein / Chlorophyll a-b binding protein 1, chloroplastic / Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Cytochrome b559 subunit alpha / Photosystem II reaction center protein H / Photosystem II reaction center protein K ...Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / (thale cress) hypothetical protein / Chlorophyll a-b binding protein 1, chloroplastic / Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Cytochrome b559 subunit alpha / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II reaction center protein Z / Photosystem II reaction center protein L / Photosystem II reaction center protein T / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein M / Photosystem II protein D1 / Chlorophyll a-b binding protein CP29.1, chloroplastic / Photosystem II reaction center W protein, chloroplastic / Photosystem II 5 kDa protein, chloroplastic / Chlorophyll a-b binding protein 3, chloroplastic / Chlorophyll a-b binding protein CP26, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsChen SJB / Wu C / Wu JH / Sui SF / Zhang LX
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Coordinates of Cryo-EM structure of the Arabidopsis thaliana C2S2M2-type PSII supercomplex
Authors: Chen SJB / Wu C / Wu JH / Sui SF / Zhang LX
History
DepositionJan 7, 2025-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63018.png

Downloads & links

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Map

FileDownload / File: emd_63018.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.35 Å/pix.
x 432 pix.
= 583.2 Å		1.35 Å/pix.
x 432 pix.
= 583.2 Å		1.35 Å/pix.
x 432 pix.
= 583.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.62
Minimum - Maximum-23.600860000000001 - 57.685886000000004
Average (Standard dev.)0.02746084 (±1.3427253)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 583.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of the Arabidopsis thaliana photosystem II(PSII...

EntireName: Cryo-EM structure of the Arabidopsis thaliana photosystem II(PSII-LHCII-ST2)
Components
  • Complex: Cryo-EM structure of the Arabidopsis thaliana photosystem II(PSII-LHCII-ST2)
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein 3, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • 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: Chlorophyll a-b binding protein 1, chloroplastic
    • 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 reaction center protein M
    • Protein or peptide: Chlorophyll a-b binding protein CP29.1, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein CP26, chloroplastic
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: Photosystem II 5 kDa protein, chloroplastic
    • Protein or peptide: Photosystem II reaction center W protein, chloroplastic
    • Protein or peptide: (thale cress) hypothetical protein
    • Protein or peptide: Photosystem II reaction center protein Z
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
  • Ligand: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BETA-CAROTENE
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: FE (II) ION
  • Ligand: PHEOPHYTIN A
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: BICARBONATE ION
  • 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

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Supramolecule #1: Cryo-EM structure of the Arabidopsis thaliana photosystem II(PSII...

SupramoleculeName: Cryo-EM structure of the Arabidopsis thaliana photosystem II(PSII-LHCII-ST2)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#22
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 28.193934 KDa
SequenceString: MAASTMALSS PALTGKAVKL SPAASEVFGT GRITMRKASK PTGPSGSPWY GSDRVKYLGP FSGEPPSYLT GEFPGDYGWD TAGLSADPE TFARNRELEV IHSRWAMLGA LGCVFPELLA RNGVKFGEAV WFKAGSQIFS DGGLDYLGNP SLVHAQSILA I WATQVILM ...String:
MAASTMALSS PALTGKAVKL SPAASEVFGT GRITMRKASK PTGPSGSPWY GSDRVKYLGP FSGEPPSYLT GEFPGDYGWD TAGLSADPE TFARNRELEV IHSRWAMLGA LGCVFPELLA RNGVKFGEAV WFKAGSQIFS DGGLDYLGNP SLVHAQSILA I WATQVILM GAVEGYRVAG DGPLGEAEDL LYPGGSFDPL GLATDPEAFA ELKVKELKNG RLAMFSMFGF FVQAIVTGKG PL ENLADHL ADPVNNNAWA FATNFVPGK

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #2: Chlorophyll a-b binding protein 3, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 3, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 26.45299 KDa
SequenceString: ASSFNPLRDV VSLGSPKYTM GNDLWYGPDR VKYLGPFSVQ TPSYLTGEFP GDYGWDTAGL SADPEAFAKN RALEVIHGRW AMLGAFGCI TPEVLQKWVR VDFKEPVWFK AGSQIFSEGG LDYLGNPNLV HAQSILAVLG FQVILMGLVE GFRINGLDGV G EGNDLYPG ...String:
ASSFNPLRDV VSLGSPKYTM GNDLWYGPDR VKYLGPFSVQ TPSYLTGEFP GDYGWDTAGL SADPEAFAKN RALEVIHGRW AMLGAFGCI TPEVLQKWVR VDFKEPVWFK AGSQIFSEGG LDYLGNPNLV HAQSILAVLG FQVILMGLVE GFRINGLDGV G EGNDLYPG GQYFDPLGLA DDPVTFAELK VKEIKNGRLA MFSMFGFFVQ AIVTGKGPLE NLLDHLDNPV ANNAWAFATK FA PGA

UniProtKB: Chlorophyll a-b binding protein 3, chloroplastic

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Macromolecule #3: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 23.198287 KDa
SequenceString: AAAAAQPKKS WIPAVKGGGN FLDPEWLDGS LPGDFGFDPL GLGKDPAFLK WYREAELIHG RWAMAAVLGI FVGQAWSGVA WFEAGAQPD AIAPFSFGSL LGTQLLLMGW VESKRWVDFF NPDSQSVEWA TPWSKTAENF ANYTGDQGYP GGRFFDPLGL A GKNRDGVY ...String:
AAAAAQPKKS WIPAVKGGGN FLDPEWLDGS LPGDFGFDPL GLGKDPAFLK WYREAELIHG RWAMAAVLGI FVGQAWSGVA WFEAGAQPD AIAPFSFGSL LGTQLLLMGW VESKRWVDFF NPDSQSVEWA TPWSKTAENF ANYTGDQGYP GGRFFDPLGL A GKNRDGVY EPDFEKLERL KLAEIKHSRL AMVAMLIFYF EAGQGKTPLG ALGL

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #4: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 38.830082 KDa
SequenceString: TAILERRESE SLWGRFCNWI TSTENRLYIG WFGVLMIPTL LTATSVFIIA FIAAPPVDID GIREPVSGSL LYGNNIISGA IIPTSAAIG LHFYPIWEAA SVDEWLYNGG PYELIVLHFL LGVACYMGRE WELSFRLGMR PWIAVAYSAP VAAATAVFLI Y PIGQGSFS ...String:
TAILERRESE SLWGRFCNWI TSTENRLYIG WFGVLMIPTL LTATSVFIIA FIAAPPVDID GIREPVSGSL LYGNNIISGA IIPTSAAIG LHFYPIWEAA SVDEWLYNGG PYELIVLHFL LGVACYMGRE WELSFRLGMR PWIAVAYSAP VAAATAVFLI Y PIGQGSFS DGMPLGISGT FNFMIVFQAE HNILMHPFHM LGVAGVFGGS LFSAMHGSLV TSSLIRETTE NESANEGYRF GQ EEETYNI VAAHGYFGRL IFQYASFNNS RSLHFFLAAW PVVGIWFTAL GISTMAFNLN GFNFNQSVVD SQGRVINTWA DII NRANLG MEVMHERNAH NFPLDLAAVE APSTNG

UniProtKB: Photosystem II protein D1

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Macromolecule #5: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 56.091824 KDa
SequenceString: MGLPWYRVHT VVLNDPGRLL AVHIMHTALV AGWAGSMALY ELAVFDPSDP VLDPMWRQGM FVIPFMTRLG ITNSWGGWNI TGGTITNPG LWSYEGVAGA HIVFSGLCFL AAIWHWVYWD LEIFCDERTG KPSLDLPKIF GIHLFLSGVA CFGFGAFHVT G LYGPGIWV ...String:
MGLPWYRVHT VVLNDPGRLL AVHIMHTALV AGWAGSMALY ELAVFDPSDP VLDPMWRQGM FVIPFMTRLG ITNSWGGWNI TGGTITNPG LWSYEGVAGA HIVFSGLCFL AAIWHWVYWD LEIFCDERTG KPSLDLPKIF GIHLFLSGVA CFGFGAFHVT G LYGPGIWV SDPYGLTGKV QPVNPAWGVE GFDPFVPGGI ASHHIAAGTL GILAGLFHLS VRPPQRLYKG LRMGNIETVL SS SIAAVFF AAFVVAGTMW YGSATTPIEL FGPTRYQWDQ GYFQQEIYRR VSAGLAENQS LSEAWAKIPE KLAFYDYIGN NPA KGGLFR AGSMDNGDGI AVGWLGHPVF RNKEGRELFV RRMPTFFETF PVVLVDGDGI VRADVPFRRA ESKYSVEQVG VTVE FYGGE LNGVSYSDPA TVKKYARRAQ LGEIFELDRA TLKSDGVFRS SPRGWFTFGH ASFALLFFFG HIWHGARTLF RDVFA GIDP DLDAQVEFGA FQKLGDPTTK RQAV

UniProtKB: Photosystem II CP47 reaction center protein

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Macromolecule #6: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 50.086324 KDa
SequenceString: TLFNGTLALA GRDQETTGFA WWAGNARLIN LSGKLLGAHV AHAGLIVFWA GAMNLFEVAH FVPEKPMYEQ GLILLPHLAT LGWGVGPGG EVIDTFPYFV SGVLHLISSA VLGFGGIYHA LLGPETLEES FPFFGYVWKD RNKMTTILGI HLILLGVGAF L LVFKALYF ...String:
TLFNGTLALA GRDQETTGFA WWAGNARLIN LSGKLLGAHV AHAGLIVFWA GAMNLFEVAH FVPEKPMYEQ GLILLPHLAT LGWGVGPGG EVIDTFPYFV SGVLHLISSA VLGFGGIYHA LLGPETLEES FPFFGYVWKD RNKMTTILGI HLILLGVGAF L LVFKALYF GGVYDTWAPG GGDVRKITNL TLSPSVIFGY LLKSPFGGEG WIVSVDDLED IIGGHVWLGS ICIFGGIWHI LT KPFAWAR RALVWSGEAY LSYSLAALSV CGFIACCFVW FNNTAYPSEF YGPTGPEASQ AQAFTFLVRD QRLGANVGSA QGP TGLGKY LMRSPTGEVI FGGETMRFWD LRAPWLEPLR GPNGLDLSRL KKDIQPWQER RSAEYMTHAP LGSLNSVGGV ATEI NAVNY VSPRSWLSTS HFVLGFFLFV GHLWHAGRAR AAAAGFEKGI DRDFEPVLSM TPLN

UniProtKB: Photosystem II CP43 reaction center protein

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Macromolecule #7: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 39.444082 KDa
SequenceString: TIALGKFTKD EKDLFDIMDD WLRRDRFVFV GWSGLLLFPC AYFALGGWFT GTTFVTSWYT HGLASSYLEG CNFLTAAVST PANSLAHSL LLLWGPEAQG DFTRWCQLGG LWAFVALHGA FALIGFMLRQ FELARSVQLR PYNAIAFSGP IAVFVSVFLI Y PLGQSGWF ...String:
TIALGKFTKD EKDLFDIMDD WLRRDRFVFV GWSGLLLFPC AYFALGGWFT GTTFVTSWYT HGLASSYLEG CNFLTAAVST PANSLAHSL LLLWGPEAQG DFTRWCQLGG LWAFVALHGA FALIGFMLRQ FELARSVQLR PYNAIAFSGP IAVFVSVFLI Y PLGQSGWF FAPSFGVAAI FRFILFFQGF HNWTLNPFHM MGVAGVLGAA LLCAIHGATV ENTLFEDGDG ANTFRAFNPT QA EETYSMV TANRFWSQIF GVAFSNKRWL HFFMLFVPVT GLWMSALGVV GLALNLRAYD FVSQEIRAAE DPEFETFYTK NIL LNEGIR AWMAAQDQPH ENLIFPEEVL PRGNAL

UniProtKB: Photosystem II D2 protein

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Macromolecule #8: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 9.393501 KDa
SequenceString:
MSGSTGERSF ADIITSIRYW VIHSITIPSL FIAGWLFVST GLAYDVFGSP RPNEYFTESR QGIPLITGRF DSLEQLDEFS RSF

UniProtKB: Cytochrome b559 subunit alpha

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Macromolecule #9: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 4.428228 KDa
SequenceString:
MTIDRTYPIF TVRWLAVHGL AVPTVSFLGS ISAMQFIQR

UniProtKB: Cytochrome b559 subunit beta

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Macromolecule #10: Chlorophyll a-b binding protein 1, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 1, chloroplastic / type: protein_or_peptide / ID: 10 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 24.885072 KDa
SequenceString: RKTVAKPKGP SGSPWYGSDR VKYLGPFSGE SPSYLTGEFP GDYGWDTAGL SADPETFARN RELEVIHSRW AMLGALGCVF PELLARNGV KFGEAVWFKA GSQIFSDGGL DYLGNPSLVH AQSILAIWAT QVILMGAVEG YRVAGNGPLG EAEDLLYPGG S FDPLGLAT ...String:
RKTVAKPKGP SGSPWYGSDR VKYLGPFSGE SPSYLTGEFP GDYGWDTAGL SADPETFARN RELEVIHSRW AMLGALGCVF PELLARNGV KFGEAVWFKA GSQIFSDGGL DYLGNPSLVH AQSILAIWAT QVILMGAVEG YRVAGNGPLG EAEDLLYPGG S FDPLGLAT DPEAFAELKV KELKNGRLAM FSMFGFFVQA IVTGKGPIEN LADHLADPVN NNAWAFATNF VPGK

UniProtKB: Chlorophyll a-b binding protein 1, chloroplastic

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Macromolecule #11: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 7.575691 KDa
SequenceString:
ATQTVEDSSR SGPRSTTVGK LLKPLNSEYG KVAPGWGTTP LMGVAMALFA VFLSIILEIY NSSVLLDGIS VN

UniProtKB: Photosystem II reaction center protein H

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Macromolecule #12: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 4.170891 KDa
SequenceString:
MLTLKLFVYT VVIFFVSLFI FGFLSNDPGR NPGREE

UniProtKB: Photosystem II reaction center protein I

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Macromolecule #13: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 4.239112 KDa
SequenceString:
KLPEAYAFLN PIVDVMPVIP LFFLLLAFVW QAAVSFR

UniProtKB: Photosystem II reaction center protein K

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Macromolecule #14: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 4.471075 KDa
SequenceString:
MTQSNPNEQS VELNRTSLYW GLLLIFVLAV LFSNYFFN

UniProtKB: Photosystem II reaction center protein L

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Macromolecule #15: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 3.783538 KDa
SequenceString:
MEVNILAFIA TALFILVPTA FLLIIYVKTV SQND

UniProtKB: Photosystem II reaction center protein M

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Macromolecule #16: Chlorophyll a-b binding protein CP29.1, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein CP29.1, chloroplastic / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 27.302855 KDa
SequenceString: AAPKKSAKKT VTTDRPLWYP GAISPDWLDG SLVGDYGFDP FGLGKPAEYL QFDIDSLDQN LAKNLAGDVI GTRTEAADAK STPFQPYSE VFGIQRFREC ELIHGRWAML ATLGALSVEW LTGVTWQDAG KVELVDGSSY LGQPLPFSIS TLIWIEVLVI G YIEFQRNA ...String:
AAPKKSAKKT VTTDRPLWYP GAISPDWLDG SLVGDYGFDP FGLGKPAEYL QFDIDSLDQN LAKNLAGDVI GTRTEAADAK STPFQPYSE VFGIQRFREC ELIHGRWAML ATLGALSVEW LTGVTWQDAG KVELVDGSSY LGQPLPFSIS TLIWIEVLVI G YIEFQRNA ELDSEKRLYP GGKFFDPLGL AADPEKTAQL QLAEIKHARL AMVAFLGFAV QAAATGKGPL NNWATHLSDP LH TTIIDTF SSS

UniProtKB: Chlorophyll a-b binding protein CP29.1, chloroplastic

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Macromolecule #17: Chlorophyll a-b binding protein CP26, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein CP26, chloroplastic / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 25.232754 KDa
SequenceString: SKAVSETSDE LAKWYGPDRR IFLPDGLLDR SEIPEYLNGE VAGDYGYDPF GLGKKPENFA KYQAFELIHA RWAMLGAAGF IIPEALNKY GANCGPEAVW FKTGALLLDG NTLNYFGKNI PINLVLAVVA EVVLLGGAEY YRITNGLDFE DKLHPGGPFD P LGLAKDPE ...String:
SKAVSETSDE LAKWYGPDRR IFLPDGLLDR SEIPEYLNGE VAGDYGYDPF GLGKKPENFA KYQAFELIHA RWAMLGAAGF IIPEALNKY GANCGPEAVW FKTGALLLDG NTLNYFGKNI PINLVLAVVA EVVLLGGAEY YRITNGLDFE DKLHPGGPFD P LGLAKDPE QGALLKVKEI KNGRLAMFAM LGFFIQAYVT GEGPVENLAK HLSDPFGNNL LTVIAGTAER APTL

UniProtKB: Chlorophyll a-b binding protein CP26, chloroplastic

+
Macromolecule #18: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 3.825642 KDa
SequenceString:
MEALVYTFLL VSTLGIIFFA IFFREPPKIS TKK

UniProtKB: Photosystem II reaction center protein T

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Macromolecule #19: Photosystem II 5 kDa protein, chloroplastic

MacromoleculeName: Photosystem II 5 kDa protein, chloroplastic / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 3.17881 KDa
SequenceString:
EPKRGTEAAK KKYAQVCVTM PTAKICRY

UniProtKB: Photosystem II 5 kDa protein, chloroplastic

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Macromolecule #20: Photosystem II reaction center W protein, chloroplastic

MacromoleculeName: Photosystem II reaction center W protein, chloroplastic
type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 6.036749 KDa
SequenceString:
LVDERMSTEG TGLPFGLSNN LLGWILFGVF GLIWTFFFVY TSSLEEDEES GLSL

UniProtKB: Photosystem II reaction center W protein, chloroplastic

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Macromolecule #21: (thale cress) hypothetical protein

MacromoleculeName: (thale cress) hypothetical protein / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 4.186916 KDa
SequenceString:
AGSGISPSLK NFLLSIASGG LVLTVIIGVV VGVSNFDPVK RT

UniProtKB: (thale cress) hypothetical protein

+
Macromolecule #22: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 6.569768 KDa
SequenceString:
MTIAFQLAVF ALIITSSILL ISVPVVFASP DGWSSNKNVV FSGTSLWIGL VFLVGILNSL IS

UniProtKB: Photosystem II reaction center protein Z

+
Macromolecule #23: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 23 / Number of copies: 95 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Macromolecule #24: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 24 / Number of copies: 215 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #25: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

MacromoleculeName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 25 / Number of copies: 31 / Formula: LUT
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-LUT:
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

+
Macromolecule #26: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...

MacromoleculeName: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
type: ligand / ID: 26 / Number of copies: 11 / Formula: NEX
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-NEX:
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL

+
Macromolecule #27: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

MacromoleculeName: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 27 / Number of copies: 5 / Formula: XAT
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-XAT:
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Macromolecule #28: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 28 / Number of copies: 22 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #29: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 29 / Number of copies: 24 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #30: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 30 / Number of copies: 2 / Formula: OEX
Molecular weightTheoretical: 339.827 Da
Chemical component information

ChemComp-OEX:
CA-MN4-O5 CLUSTER

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Macromolecule #31: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 31 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #32: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 32 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 33 / Number of copies: 10 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #34: 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: 34 / Number of copies: 8 / 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 #35: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 35 / Number of copies: 9 / 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

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Macromolecule #37: 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: 37 / Number of copies: 2 / 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 #38: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 38 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 38544
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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