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- EMDB-52077: Universal Photosystem II Intermediate with Light-Dependent Water-... -

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Basic information

Entry
Database: EMDB / ID: EMD-52077
TitleUniversal Photosystem II Intermediate with Light-Dependent Water-Ferrocyanide Oxydo-reductase activity from Chlamydomonas reinhardtii
Map data
Sample
  • Complex: Photosystem II Intermediate
    • Protein or peptide: x 21 types
  • Ligand: x 15 types
KeywordsGreen alga / PSII / Chlamydomonas reinhardtii / membrane protein / Cryo-EM / PHOTOSYNTHESIS / assembly intermediate / water-ferrocyanide oxido-reductase.
Function / homology
Function and homology information


photosystem II repair / chloroplast thylakoid lumen / 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 repair / chloroplast thylakoid lumen / 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 / extrinsic component of membrane / response to herbicide / : / chlorophyll binding / photosynthetic electron transport in photosystem II / phosphate ion binding / photosynthesis, light reaction / chloroplast thylakoid membrane / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / calcium ion binding / metal ion binding
Similarity search - Function
Photosystem II Pbs27 / Photosystem II Pbs27 superfamily / Photosystem II Pbs27 / PsbP, C-terminal / : / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Oxygen-evolving enhancer protein 3 ...Photosystem II Pbs27 / Photosystem II Pbs27 superfamily / Photosystem II Pbs27 / PsbP, C-terminal / : / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / 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 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 reaction centre protein H superfamily / 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 / Photosystem II 10 kDa phosphoprotein / 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
Uncharacterized protein / Uncharacterized protein / Photosystem II reaction center protein J / Photosystem II D2 protein / Photosystem II protein D1 / Photosystem II CP43 reaction center protein / Oxygen-evolving enhancer protein 2, chloroplastic / Oxygen-evolving enhancer protein 3, chloroplastic / Oxygen-evolving enhancer protein 1, chloroplastic / Photosystem II reaction center protein K ...Uncharacterized protein / Uncharacterized protein / Photosystem II reaction center protein J / Photosystem II D2 protein / Photosystem II protein D1 / Photosystem II CP43 reaction center protein / Oxygen-evolving enhancer protein 2, chloroplastic / Oxygen-evolving enhancer protein 3, chloroplastic / Oxygen-evolving enhancer protein 1, chloroplastic / Photosystem II reaction center protein K / Photosystem II reaction center protein H / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein T / Cytochrome b559 subunit alpha / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein I / Photosystem II reaction center protein Z / Photosystem II reaction center protein M / Cytochrome b559 subunit beta / Photosystem II reaction center protein L / Photosystem II reaction center W protein, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsNelson N / Klaiman D / Fadeeva M / Kandiah E
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
CitationJournal: To Be Published
Title: Universal Photosystem II Intermediate with Light-Dependent Water-Ferrocyanide Oxydo-reductase activity from Chlamydomonas reinhardtii
Authors: Nelson N / Klaiman D / Fadeeva M / Kandiah E
History
DepositionNov 14, 2024-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52077.png

Downloads & links

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Map

FileDownload / File: emd_52077.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 250 pix.
= 210. Å		0.84 Å/pix.
x 250 pix.
= 210. Å		0.84 Å/pix.
x 250 pix.
= 210. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.012692612 - 0.040538415
Average (Standard dev.)0.0004711195 (±0.0024013857)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 210.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52077_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_52077_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 Intermediate

EntireName: Photosystem II Intermediate
Components
  • Complex: Photosystem II Intermediate
    • 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: Oxygen-evolving enhancer protein 1, chloroplastic
    • Protein or peptide: Oxygen-evolving enhancer protein 2, chloroplastic
    • Protein or peptide: Oxygen-evolving enhancer protein 3, chloroplastic
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: 4.1 kDa photosystem II subunit
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: Photosystem II reaction center protein U
    • Protein or peptide: Photosystem II reaction center W protein, chloroplastic
  • 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: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • 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
  • Ligand: water

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Supramolecule #1: Photosystem II Intermediate

SupramoleculeName: Photosystem II Intermediate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organelle: Chloroplast
Molecular weightTheoretical: 400 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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 37.058215 KDa
SequenceString: SSLWARFCEW ITSTENRLYI GWFGVIMIPC LLTATSVFII AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVIPTSNAIG LHFYPIWEA ASLDEWLYNG GPYQLIVCHF LLGVYCYMGR EWELSFRLGM RPWIAVAYSA PVAAASAVFL VYPIGQGSFS D GMPLGISG ...String:
SSLWARFCEW ITSTENRLYI GWFGVIMIPC LLTATSVFII AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVIPTSNAIG LHFYPIWEA ASLDEWLYNG GPYQLIVCHF LLGVYCYMGR EWELSFRLGM RPWIAVAYSA PVAAASAVFL VYPIGQGSFS D GMPLGISG TFNFMIVFQA EHNILMHPFH MLGVAGVFGG SLFSAMHGSL VTSSLIRETT ENESANEGYR FGQEEETYNI VA AHGYFGR LIFQYASFNN SRSLHFFLAA WPVIGIWFTA LGLSTMAFNL NGFNFNQSVV DSQGRVLNTW ADIINRANLG MEV MHERNA HNFPLDLA

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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 52.938281 KDa
SequenceString: GLPWYRVHTV VINDPGRLIS VHLMHTALVS GWAGSMALFE ISVFDPSDPV LNPMWRQGMF VLPFMTRLGI TQSWGGWTIS GETATNPGI WSYEGVAAAH IILSGALFLA SVWHWTYWDL ELFRDPRTGK TALDLPKIFG IHLFLSGLLC FGFGAFHVTG V FGPGIWVS ...String:
GLPWYRVHTV VINDPGRLIS VHLMHTALVS GWAGSMALFE ISVFDPSDPV LNPMWRQGMF VLPFMTRLGI TQSWGGWTIS GETATNPGI WSYEGVAAAH IILSGALFLA SVWHWTYWDL ELFRDPRTGK TALDLPKIFG IHLFLSGLLC FGFGAFHVTG V FGPGIWVS DPYGLTGRVQ PVAPSWGADG FDPYNPGGIA SHHIAAGILG VLAGLFHLCV RPSIRLYFGL SMGSIETVLS SS IAAVFWA AFVVAGTMWY GSAATPIELF GPTRYQWDQG FFQQEIQKRV QASLAEGASL SDAWSRIPEK LAFYDYIGNN PAK GGLFRT GAMNSGDGIA VGWLGHASFK DQEGRELFVR RMPTFFETFP VLLLDKDGIV RADVPFRKAE SKYSIEQVGV SVTF YGGEL DGLTFTDPAT VKKYARKAQL GEIFEFDRST LQSDGVFRSS PRGWFTFGHV CFALLFFFGH IWHGARTIFR DVFAG

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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.201863 KDa
SequenceString:
NIELALTLVS LVLVVSAGPL VVVLLSARGG NL

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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 49.416305 KDa
SequenceString: GRDQETTGFA WWSGNARLIN LSGKLLGAHV AHAGLIVFWA GAMNLFEVSH FVPEKPMYEQ GLILLPHIAT LGYGVGPGGE IIDTFPYFV SGVLHLISSA VLGFGGVYHS LIGPETLEES YPFFGYVWKD KNKMTNILGY HLIMLGLGAW LLVWKAMYFG G VYDTWAPG ...String:
GRDQETTGFA WWSGNARLIN LSGKLLGAHV AHAGLIVFWA GAMNLFEVSH FVPEKPMYEQ GLILLPHIAT LGYGVGPGGE IIDTFPYFV SGVLHLISSA VLGFGGVYHS LIGPETLEES YPFFGYVWKD KNKMTNILGY HLIMLGLGAW LLVWKAMYFG G VYDTWAPG GGDVRVITNP TTNAAVIFGY LVKSPFGGDG WICSVDNMED IIGGHIWIGT LEILGGIWHI YTTPWPWARR AF VWSGEAY LSYSLGAIGV MGFIACCMSW FNNTAYPSEF YGPTGPEASQ SQAFTFLVRD QRLGANVASA QGPTGLGKYL MRS PTGEII FGGETMRFWD FRGPWLEPLR GPNGLDLNKL KNDIQPWQER RAAEYMTHAP LGSLNSVGGV ATEINAVNFV SPRS WLACS HFCLGFFFFI GHLWHAGRAR AAAAGFEKGI DRFDEPVLSM 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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 39.0575 KDa
SequenceString: IGTYQEKRTW FDDADDWLRQ DRFVFVGWSG LLLFPCAYFA LGGWLTGTTF VTSWYTHGLA TSYLEGCNFL TAAVSTPANS MAHSLLFVW GPEAQGDFTR WCQLGGLWAF VALHGAFGLI GFMLRQFEIA RSVNLRPYNA IAFSAPIAVF VSVFLIYPLG Q SGWFFAPS ...String:
IGTYQEKRTW FDDADDWLRQ DRFVFVGWSG LLLFPCAYFA LGGWLTGTTF VTSWYTHGLA TSYLEGCNFL TAAVSTPANS MAHSLLFVW GPEAQGDFTR WCQLGGLWAF VALHGAFGLI GFMLRQFEIA RSVNLRPYNA IAFSAPIAVF VSVFLIYPLG Q SGWFFAPS FGVAAIFRFI LFFQGFHNWT LNPFHMMGVA GVLGAALLCA IHGATVENTL FEDGDGANTF RAFNPTQAEE TY SMVTANR FWSQIFGVAF SNKRWLHFFM LLVPVTGLWM SAIGVVGLAL NLRAYDFVSQ EIRAAEDPEF ETFYTKNILL NEG IRAWMA AQDQPHERLV FPEEVLPRGN 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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 8.598734 KDa
SequenceString:
RPFSDILTSI RYWVIHSITV PALFIAGWLF VSTGLAYDVF GTPRPNEYFT EDRQEAPLIT DRFNALEQVK KLSGN

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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.535273 KDa
SequenceString:
IFTVRWLAIH GIAVPTIFFL 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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 7.11844 KDa
SequenceString:
PGLVTPLGTL LRPLNSEAGK VLPGWGTTVL MAVFILLFAA FLLIILEIYN SSLILDDVSM SWETLA

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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.902687 KDa
SequenceString:
MLTLKIFVYT VVTFFVCLFI FGFLSNDPAR NPGK

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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.699365 KDa
SequenceString:
TGRIPLWLVG TVVGTLAIGL LAVFFYGSYV 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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.147979 KDa
SequenceString:
KLPEAYAPFA PIVDVLPVIP VFFILLAFVW QAAVSFR

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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.071762 KDa
SequenceString:
PNPNKQVVEL NRTSLYWGLL LIFVLAVLFS SYIFN

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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.157804 KDa
SequenceString:
VNIYGLTATA LFIIIPTSFL LILYVKTAS

UniProtKB: Photosystem II reaction center protein M

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Macromolecule #14: Oxygen-evolving enhancer protein 1, chloroplastic

MacromoleculeName: Oxygen-evolving enhancer protein 1, chloroplastic / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 25.704027 KDa
SequenceString: LTFDEIQGLT YLQVKGSGIA NTCPVLESGT TNLKELKAGS YKLENFCIEP TSFTVKEESQ FKGGETEFVK TKLMTRLTYT LDAMSGSFK VGSDGSAELK EDDGIDYAAT TVQLPGGERV AFLFTIKQFD GKGTLDGIKG DFLVPSYRGS SFLDPKGRGG S TGYDNAVA ...String:
LTFDEIQGLT YLQVKGSGIA NTCPVLESGT TNLKELKAGS YKLENFCIEP TSFTVKEESQ FKGGETEFVK TKLMTRLTYT LDAMSGSFK VGSDGSAELK EDDGIDYAAT TVQLPGGERV AFLFTIKQFD GKGTLDGIKG DFLVPSYRGS SFLDPKGRGG S TGYDNAVA LPARADAEEL LKENVKITKA LKGSAVFSVA KVDPVTGEIA GVFESIQPSD TDLGAKPPKD IKVTGLWYAQ LK

UniProtKB: Oxygen-evolving enhancer protein 1, chloroplastic

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Macromolecule #15: Oxygen-evolving enhancer protein 2, chloroplastic

MacromoleculeName: Oxygen-evolving enhancer protein 2, chloroplastic / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 20.440826 KDa
SequenceString:
AYGDSANVFG KVTNKSGFVP YAGDGFALLL PAKWNPSKEN DFPGVILRYE DNFDAVNNLV VIAQDTDKKA IADFGSQDKF LESVSYLLG KQAYSGETQS EGGFAPNRVS AASLLDVSTT TDKKGKTYYK YELLVRSADG DEGGRHQLIG ATVGSDNKLY I IKIQIGDK RWFKGAKKEA MGAFDSFTVV

UniProtKB: Oxygen-evolving enhancer protein 2, chloroplastic

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Macromolecule #16: Oxygen-evolving enhancer protein 3, chloroplastic

MacromoleculeName: Oxygen-evolving enhancer protein 3, chloroplastic / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 16.943199 KDa
SequenceString:
LTPVDLFDDR SVRDRGFDLI YEARDLDLPQ NVREGFTQAR ASLDETKKRV KESEARIDAD LDVFIQKSYW TEAREQLRRQ VGTLRFDLN TLASTKEKEA KKAALGLRKE FIQAVEDLDF ALREKDQASA AKKLEITKAK LDSVLAAVL

UniProtKB: Oxygen-evolving enhancer protein 3, chloroplastic

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Macromolecule #17: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.510259 KDa
SequenceString:
MEALVYTFLL VGTLGIIFFS IFFRDPPRMI

UniProtKB: Photosystem II reaction center protein T

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Macromolecule #18: 4.1 kDa photosystem II subunit

MacromoleculeName: 4.1 kDa photosystem II subunit / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.132736 KDa
SequenceString:
VTPSLKNFLG SLIAGATVLG GIALAITAVS KF

UniProtKB: Uncharacterized protein

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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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 6.466732 KDa
SequenceString:
MTSILQVALL ALIFVSFALV VGVPVVFATP NGWTDNKGAV FSGLSLWLLL VFVVGILNSF V

UniProtKB: Photosystem II reaction center protein Z

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Macromolecule #20: Photosystem II reaction center protein U

MacromoleculeName: Photosystem II reaction center protein U / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 2.531878 KDa
SequenceString:
VTLALDKDDP AKEDSVKGLR KDI

UniProtKB: Uncharacterized protein

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Macromolecule #21: Photosystem II reaction center W protein, chloroplastic

MacromoleculeName: Photosystem II reaction center W protein, chloroplastic
type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.881611 KDa
SequenceString:
LVDERMNGDG TGRPFGVNDP VLGWVLLGVF GTMWAIWFIG QKDL

UniProtKB: Photosystem II reaction center W protein, chloroplastic

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Macromolecule #22: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 22 / 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 #23: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 23 / Number of copies: 1 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #24: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 24 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #25: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 25 / Number of copies: 35 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #26: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 26 / Number of copies: 2 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #27: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 27 / Number of copies: 8 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #28: 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: 28 / Number of copies: 1 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

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

+
Macromolecule #29: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 29 / Number of copies: 5 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #30: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 30 / Number of copies: 4 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #31: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 31 / Number of copies: 3 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #32: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 32 / 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 #33: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 33 / Number of copies: 1 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION

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Macromolecule #34: 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: 34 / 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 #35: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 35 / 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 #36: water

MacromoleculeName: water / type: ligand / ID: 36 / Number of copies: 7 / 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

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Sample preparation

BufferpH: 6
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 4 / Number real images: 24435 / Average electron dose: 46.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8293123
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6kac

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 361852
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final 3D classificationNumber classes: 10 / Avg.num./class: 80846 / Software - Name: RELION (ver. 4.0.1)
FSC plot (resolution estimation)

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