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- EMDB-52846: STRUCTURE OF UNSTACKED C2S2-TYPE PSII-LHCII SUPERCOMPLEX FROM PIS... -

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Basic information

Entry
Database: EMDB / ID: EMD-52846
TitleSTRUCTURE OF UNSTACKED C2S2-TYPE PSII-LHCII SUPERCOMPLEX FROM PISUM SATIVUM
Map data
Sample
  • Complex: C2S2-TYPE PSII-LHCII SUPERCOMPLEX FROM PISUM SATIVUM
    • Protein or peptide: x 24 types
  • Ligand: x 18 types
KeywordsPlant / PSII / Pisum sativum / membrane protein / Cryo-EM / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosynthesis, light harvesting / 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 I ...photosynthesis, light harvesting / 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 I / photosystem II / extrinsic component of membrane / response to herbicide / : / photosynthetic electron transport in photosystem II / chlorophyll binding / phosphate ion binding / photosynthesis, light reaction / chloroplast thylakoid membrane / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / mRNA binding / heme binding / calcium ion binding / metal ion binding
Similarity search - Function
Photosystem II 5kDa protein, chloroplastic / 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 5kDa protein, chloroplastic / 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 PsbX, type 1 subfamily / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / 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. / : / Chlorophyll A-B binding protein, plant and chromista / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Chlorophyll A-B binding protein / Chlorophyll A-B binding 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
Chlorophyll a-b binding protein, chloroplastic / PSII 6.1 kDa protein / Photosystem II 5 kDa protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem II reaction center protein K / Photosystem II reaction center protein I / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II protein D1 ...Chlorophyll a-b binding protein, chloroplastic / PSII 6.1 kDa protein / Photosystem II 5 kDa protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem II reaction center protein K / Photosystem II reaction center protein I / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II protein D1 / Chlorophyll a-b binding protein AB80, chloroplastic / Cytochrome b559 subunit alpha / Photosystem II reaction center protein J / Oxygen-evolving enhancer protein 1, chloroplastic / Oxygen-evolving enhancer protein 2, chloroplastic / Chlorophyll a-b binding protein 8, chloroplastic / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Photosystem II reaction center protein M / Photosystem II reaction center protein Z / 16 kDa subunit of oxygen evolving system of photosystem II / Photosystem II reaction center protein T / Ultraviolet-B-repressible protein / Photosystem II reaction center protein H
Similarity search - Component
Biological speciesPisum sativum (garden pea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsKlaiman D / Fadeeva M / Kandiah E / Nelson N
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation199/21 Israel
CitationJournal: To Be Published
Title: STRUCTURE OF UNSTACKED C2S2-TYPE PSII-LHCII SUPERCOMPLEX FROM PISUM SATIVUM
Authors: Klaiman D / Fadeeva M / Nelson N
History
DepositionFeb 18, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52846.png

Downloads & links

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Map

FileDownload / File: emd_52846.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 500 pix.
= 420. Å		0.84 Å/pix.
x 500 pix.
= 420. Å		0.84 Å/pix.
x 500 pix.
= 420. 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-0.027201986 - 0.059905734
Average (Standard dev.)0.00002883489 (±0.0027838037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 420.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52846_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_52846_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 : C2S2-TYPE PSII-LHCII SUPERCOMPLEX FROM PISUM SATIVUM

EntireName: C2S2-TYPE PSII-LHCII SUPERCOMPLEX FROM PISUM SATIVUM
Components
  • Complex: C2S2-TYPE PSII-LHCII SUPERCOMPLEX FROM PISUM SATIVUM
    • 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 8, 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 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
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: Photosystem II reaction center protein W
    • Protein or peptide: Ultraviolet-B-repressible protein
    • Protein or peptide: Chlorophyll a-b binding protein AB80, chloroplastic
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: Photosystem II 5 kDa 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: 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: BICARBONATE ION
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CHLOROPHYLL B
  • 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: water

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Supramolecule #1: C2S2-TYPE PSII-LHCII SUPERCOMPLEX FROM PISUM SATIVUM

SupramoleculeName: C2S2-TYPE PSII-LHCII SUPERCOMPLEX FROM PISUM SATIVUM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#24
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 1.2 MDa

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Macromolecule #1: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 36.972074 KDa
SequenceString: ENLWGRFCNW ITSTENRLYI GWFGVLMIPT LLTATSVFII AFIAAPPVDI DGIREPVSGS LLYGNNIISG AIIPTSAAIG LHFYPIWEA ASVDEWLYNG GPYELIVLHF LLGVACYMGR EWELSFRLGM RPWIAVAYSA PVAAATAVFL IYPIGQGSFS D GMPLGISG ...String:
ENLWGRFCNW ITSTENRLYI GWFGVLMIPT LLTATSVFII AFIAAPPVDI DGIREPVSGS LLYGNNIISG AIIPTSAAIG LHFYPIWEA ASVDEWLYNG GPYELIVLHF LLGVACYMGR EWELSFRLGM RPWIAVAYSA PVAAATAVFL IYPIGQGSFS D GMPLGISG TFNFMIVFQA EHNILMHPFH MLGVAGVFGG SLFSAMHGSL VTSSLIRETT ENESANEGYR FGQEEETYNI VA AHGYFGR LIFQYASFNN SRSLHFFLAA WPVVGIWFTA LGISTMAFNL NGFNFNQSVV DSQGRVINTW 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 55.534133 KDa
SequenceString: GLPWYRVHTV VLNDPGRLLS VHIMHTALVA GWAGSMALYE LAVFDPSDPV LDPMWRQGMF VIPFMTRLGI TNSWGGWNIT GGTITNPGI WSYEGVAAAH IVFSGLCFLA AIWHWVYWDL EIFCDERTGK PSLDLPKIFG IHLFLAGVAC FGFGAFHVTG L FGPGIWVS ...String:
GLPWYRVHTV VLNDPGRLLS VHIMHTALVA GWAGSMALYE LAVFDPSDPV LDPMWRQGMF VIPFMTRLGI TNSWGGWNIT GGTITNPGI WSYEGVAAAH IVFSGLCFLA AIWHWVYWDL EIFCDERTGK PSLDLPKIFG IHLFLAGVAC FGFGAFHVTG L FGPGIWVS DPYGLTGRVQ SVNPAWGVDG FDPFVPGGIA SHHIAAGTLG ILAGLFHLSV RPPQRLYKGL RMGNIETVLS SS IAAVFFA AFVVAGTMWY GSATTPIELF GPTRYQWDQG YFQQEIYRRV GGGLVENQSL SEAWSKIPEK LAFYDYIGNN PAK GGLFRA GSMDNGDGIA VGWLGHPIFR DKEGRELFVR RMPTFFETFP VVLVDGDGIV RADVPFRRAE SKYSVEQVGV IVEF YGGEL NGVSYSDPAT VKKYARRAQL GEIFELDRAT LKSDGVFRSS PRGWFTFGHA SFALLFFFGH IWHGARTLFR DVFAG IDPD LDAQVEFGAF QKLGDPTTK

UniProtKB: Photosystem II CP47 reaction center protein

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Macromolecule #3: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 49.275371 KDa
SequenceString: TGRDQETTGF AWWAGNARLI NLSGKLLGAH VAHAGLIVFW AGAMNLFEVA HFVPEKPMYE QGLILLPHLA TLGWGVGPGG EVIDTFPYF VSGVLHLISS AVLGFGGIYH ALLGPETLEE SFPFFGYVWK DRNKMTTILG IHLILLGIGS FLLVFKAFYF G GIYDTWAP ...String:
TGRDQETTGF AWWAGNARLI NLSGKLLGAH VAHAGLIVFW AGAMNLFEVA HFVPEKPMYE QGLILLPHLA TLGWGVGPGG EVIDTFPYF VSGVLHLISS AVLGFGGIYH ALLGPETLEE SFPFFGYVWK DRNKMTTILG IHLILLGIGS FLLVFKAFYF G GIYDTWAP GGGDVRKITN FTLSPSILFG YLLKSPFGGE GWIVSVDDLE DIIGGHVWLG SICILGGIWH ILTKPFAWAR RA LVWSGEA YLSYSLGALA VFGFIACCFV WFNNTAYPSE FYGPTGPEAS QAQAFTFLVR DQRLGANVGS AQGPTGLGKY LMR SPTGEV IFGGETMRFW DLRAPWLEPL RGPNGLDLSR LKKDIQPWQE RRSAEYMTHA PLGSLNSVGG VATEINAVNY VSPR SWLAT SHFVLGFFLF VGHLWHAGRA RAAAAGFEKG IDRDFEPVLS MTPLN

UniProtKB: Photosystem II CP43 reaction center protein

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Macromolecule #4: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 39.426 KDa
SequenceString: TIALGKFTKD QNDLFDIMDD WLRRDRFVFV GWSGLLLFPC AYFAVGGWFT GTTFVTSWYT HGLASSYLEG CNFLTAAVST PANSLAHSL LLLWGPEAQG DLTRWCQLGG LWTFVALHGA FGLIGFMLRQ FELARSVQLR PYNAIAFSGP IAVFVSVFLI Y PLGQSGWF ...String:
TIALGKFTKD QNDLFDIMDD WLRRDRFVFV GWSGLLLFPC AYFAVGGWFT GTTFVTSWYT HGLASSYLEG CNFLTAAVST PANSLAHSL LLLWGPEAQG DLTRWCQLGG LWTFVALHGA FGLIGFMLRQ FELARSVQLR PYNAIAFSGP IAVFVSVFLI Y PLGQSGWF FAPSFGVAAI FRFILFFQGF HNWTLNPFHM MGVAGVLGAA LLCAIHGATV ENTLFEDGDG ANTFRAFNPT QA EETYSMV TANRFWSQIF GVAFSNKRWL HFFMLFVPVT GLWMSALGVV GLALNLRAYD FVSQEIRAAE DPEFETFYTK NIL LNEGIR AWMATQDQPH ENLIFPEEVL PRGNAL

UniProtKB: Photosystem II D2 protein

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Macromolecule #5: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 8.624707 KDa
SequenceString:
RSFADIITSI RYWIIHSITI PSLFIAGWLF VSTGLAYDVF GSPRPNEYFT ETRQGIPLIT GRFDSLEQLD EFSRS

UniProtKB: Cytochrome b559 subunit alpha

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Macromolecule #6: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.396035 KDa
SequenceString:
FTVRWLAVHG LAVPTVFFLG SISAMQFIQR

UniProtKB: Cytochrome b559 subunit beta

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Macromolecule #7: Chlorophyll a-b binding protein 8, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 8, chloroplastic / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 23.320176 KDa
SequenceString: GSPWYGPDRV KYLGPFSGES PSYLTGEFPG DYGWDTAGLS ADPETFSKNR ELEVIHSRWA MLGALGCVFP ELLSRNGVKF GEAVWFKAG SQIFSEGGLD YLGNPSLVHA QSILAIWATQ VILMGAVEGY RIAGGPLGEV VDPLYPGGSF DPLGLADDPE A FAELKVKE ...String:
GSPWYGPDRV KYLGPFSGES PSYLTGEFPG DYGWDTAGLS ADPETFSKNR ELEVIHSRWA MLGALGCVFP ELLSRNGVKF GEAVWFKAG SQIFSEGGLD YLGNPSLVHA QSILAIWATQ VILMGAVEGY RIAGGPLGEV VDPLYPGGSF DPLGLADDPE A FAELKVKE LKNGRLAMFS MFGFFVQAIV TGKGPLENLA DHLSDPVNNN AWSYATNF

UniProtKB: Chlorophyll a-b binding protein 8, chloroplastic

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 6.455607 KDa
SequenceString:
GPRRTAVGDL LKPLNSEYGK VAPGWGTTPL MGIAMALFAV FLSIILEIYN SSLLLDQISM

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: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.926691 KDa
SequenceString:
MLTLKLFVYT IVIFFVSLFI FGFLSNDPGR NPGR

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: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.598264 KDa
SequenceString:
GRIPLWIIGT VAGIVVIGLI GLFFYGSYSG LGSSL

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: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 4.287155 KDa
SequenceString:
KLPEAYAFLN PIVDFMPVIP LLFFLLAFVW 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 4.2658 KDa
SequenceString:
QSNPNEQNVE LNRTSLYWGL LLIFVLAVLF SNYFFN

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: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.641425 KDa
SequenceString:
MEVNILAFIA TALFILVPTA FLLIIYVKTV SQS

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: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 26.554646 KDa
SequenceString: EGAPKRLTFD EIQSKTYLEV KGTGTANQCP TIDGGVDSFS FKPGKYNAKK LCLEPTSFTV KSEGVTKNTP LAFQNTKLMT RLTYTLDEI EGPFEVSADG SVKFEEKDGI DYAAVTVQLP GGERVPFLFT IKQLVASGKP DSFSGEFLVP SYRGSSFLDP K GRGASTGY ...String:
EGAPKRLTFD EIQSKTYLEV KGTGTANQCP TIDGGVDSFS FKPGKYNAKK LCLEPTSFTV KSEGVTKNTP LAFQNTKLMT RLTYTLDEI EGPFEVSADG SVKFEEKDGI DYAAVTVQLP GGERVPFLFT IKQLVASGKP DSFSGEFLVP SYRGSSFLDP K GRGASTGY DNAVALPAGG RGDEEELGKE NNKSAASSKG KITLSVTQTK PETGEVIGVF ESIQPSDTDL GAKAPKDVKI QG VWYAQLE S

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: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 20.287494 KDa
SequenceString:
AYGEAANVFG KAKTNTDYLP YNGDGFKLLV PAKWNPSKER EFPGQVLRYE DNFDATSNVS VLVQTTDKKS ITDYGSPEEF LSKVDYLLG KQAFFGQTDS EGGFDTNAVA VANILESSAP VIGGKQYYNI SVLTRTADGD EGGKHQLITA TVKDGKLYIC K AQAGDKRW FKGARKFVED TASSFSVA

UniProtKB: Oxygen-evolving enhancer protein 2, chloroplastic

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Macromolecule #16: Oxygen-evolving enhancer protein 3

MacromoleculeName: Oxygen-evolving enhancer protein 3 / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 16.398898 KDa
SequenceString:
EAIPIKVGGP PPLSGGLPGT LNSDEARDLK LPLKERFFIQ PLAPTEAAAR TKESAKEIVA AKKFIDQKAW PFLQNDLRLR AGYLRYDLK TIISSKPKDQ KQSLKELTDK LFQDISNLDH AAKIKSPSEA EKYYAIAVST LNDVLSKIA

UniProtKB: 16 kDa subunit of oxygen evolving system of photosystem II

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

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 24.791123 KDa
SequenceString: RPLWFPGAKS PEYLDGSLVG DYGFDPFGLG KPAEYLQFDL DSLDQNLAKN LAGDVIGTRT EFEDVKSTPF QPYTEVFGLQ RFRECELIH GRWAMLATLG ALTVEWLTGV TWQDAGKVEL VEGSTYLGQP LPFSITTLIW IEVLVIGYIE FQRNAELDSE K RLYPGGKF ...String:
RPLWFPGAKS PEYLDGSLVG DYGFDPFGLG KPAEYLQFDL DSLDQNLAKN LAGDVIGTRT EFEDVKSTPF QPYTEVFGLQ RFRECELIH GRWAMLATLG ALTVEWLTGV TWQDAGKVEL VEGSTYLGQP LPFSITTLIW IEVLVIGYIE FQRNAELDSE K RLYPGGKF FDPLGLAADP EKKATLQLAE IKHARLAMVA FLGFAVQAAA TGKGPLNNWA THLSDP

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #18: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 23.839139 KDa
SequenceString: ANEELAKWYG PDRRIFLPDG LLDRSEIPEY LTGEVPGDYG YDPFGLSKKP EDFAKYQGYE LIHARWAMLG AAGFIIPEAF NKYGANCGP EAVWFKTGAL LLDGGTLNYF GKPIPINLIL AVVAEVVLLG GAEYYRITNG LDLEDKFHPG GPFDPLGLAN D PDQAAILK ...String:
ANEELAKWYG PDRRIFLPDG LLDRSEIPEY LTGEVPGDYG YDPFGLSKKP EDFAKYQGYE LIHARWAMLG AAGFIIPEAF NKYGANCGP EAVWFKTGAL LLDGGTLNYF GKPIPINLIL AVVAEVVLLG GAEYYRITNG LDLEDKFHPG GPFDPLGLAN D PDQAAILK VKEIKNGRLA MFAMLGFFIQ AYVTGEGPVE NFAKHLSDPF GNNLLTVIAG

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #19: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.563292 KDa
SequenceString:
MEALVYTFLL VSTLGIIFFA IFFREPPKVP T

UniProtKB: Photosystem II reaction center protein T

+
Macromolecule #20: Photosystem II reaction center protein W

MacromoleculeName: Photosystem II reaction center protein W / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 5.914629 KDa
SequenceString:
LVDDRMSTEG TGLPFGLSNN LLGWILFGVF GLIWALYFIY ASGLDEDEES GLSL

UniProtKB: PSII 6.1 kDa protein

+
Macromolecule #21: Ultraviolet-B-repressible protein

MacromoleculeName: Ultraviolet-B-repressible protein / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.929627 KDa
SequenceString:
ATVSPSLKNF LLSIVSGGVV VTAILGAVIG VSNFDPVKR

UniProtKB: Ultraviolet-B-repressible protein

+
Macromolecule #22: Chlorophyll a-b binding protein AB80, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein AB80, chloroplastic / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 23.557473 KDa
SequenceString: GSPWYGPDRV KYLGPFSGES PSYLTGEFPG DYGWDTAGLS ADPETFSKNR ELEVIHSRWA MLGALGCVFP ELLSRNGVKF GEAVWFKAG SQIFSEGGLD YLGNPSLVHA QSILAIWATQ VILMGAVEGY RIAGGPLGEV VDPLYPGGSF DPLGLADDPE A FAELKVKE ...String:
GSPWYGPDRV KYLGPFSGES PSYLTGEFPG DYGWDTAGLS ADPETFSKNR ELEVIHSRWA MLGALGCVFP ELLSRNGVKF GEAVWFKAG SQIFSEGGLD YLGNPSLVHA QSILAIWATQ VILMGAVEGY RIAGGPLGEV VDPLYPGGSF DPLGLADDPE A FAELKVKE LKNGRLAMFS MFGFFVQAIV TGKGPLENLA DHLADPVNNN AWSYATNFVP G

UniProtKB: Chlorophyll a-b binding protein AB80, chloroplastic

+
Macromolecule #23: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 23 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 6.468664 KDa
SequenceString:
MTIAFQLAVF ALIVTSSILL ISVPVVFASP DGWSSNKNVV FSGTSLWIGL VFLVGILNSL I

UniProtKB: Photosystem II reaction center protein Z

+
Macromolecule #24: Photosystem II 5 kDa protein, chloroplastic

MacromoleculeName: Photosystem II 5 kDa protein, chloroplastic / type: protein_or_peptide / ID: 24 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.080648 KDa
SequenceString:
EPKRGSPEAK KAYAPVCVTM PTARICRN

UniProtKB: Photosystem II 5 kDa protein, chloroplastic

+
Macromolecule #25: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 25 / Number of copies: 2 / Formula: OEX
Molecular weightTheoretical: 339.827 Da
Chemical component information

ChemComp-OEX:
CA-MN4-O5 CLUSTER

+
Macromolecule #26: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 26 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #27: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 27 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 Da

+
Macromolecule #28: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 28 / Number of copies: 156 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #29: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 29 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

+
Macromolecule #30: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 30 / Number of copies: 22 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #31: 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: 31 / 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

+
Macromolecule #32: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 32 / Number of copies: 14 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #33: 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: 33 / Number of copies: 4 / Formula: PL9
Molecular weightTheoretical: 749.201 Da
Chemical component information

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

+
Macromolecule #34: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 34 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

+
Macromolecule #35: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 35 / Number of copies: 28 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #36: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 36 / Number of copies: 10 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #37: PROTOPORPHYRIN IX CONTAINING FE

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

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

+
Macromolecule #38: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 38 / Number of copies: 50 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

+
Macromolecule #39: (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: 39 / Number of copies: 18 / 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 #40: (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: 40 / Number of copies: 9 / 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 #41: (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: 41 / Number of copies: 4 / 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

+
Macromolecule #42: water

MacromoleculeName: water / type: ligand / ID: 42 / Number of copies: 1711 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 288 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 29624 / Average exposure time: 1.5 sec. / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 5998672
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5xnl

Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.0) / Number images used: 200827
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: 6 / Avg.num./class: 33471 / Software - Name: RELION (ver. 4.0.0)
FSC plot (resolution estimation)

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