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- EMDB-10865: PSII-LHCII C2S2 supercomplex from Pisum sativum grown in high lig... -

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Basic information

Entry
Database: EMDB / ID: EMD-10865
TitlePSII-LHCII C2S2 supercomplex from Pisum sativum grown in high light conditions
Map dataPSIILHCII C2S2 supercomplex in high light condition
Sample
  • Complex: PSII-LHCII C2S2 supercomplex
    • Protein or peptide: x 20 types
  • Ligand: x 17 types
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I ...photosynthesis, light harvesting / photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily ...Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbM / 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 CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / 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 / Chlorophyll A-B binding protein, plant and chromista / 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 reaction center protein K / Photosystem II reaction center protein I / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II protein D1 / Cytochrome b559 subunit alpha / Photosystem II reaction center protein J / Oxygen-evolving enhancer protein 1, chloroplastic ...Chlorophyll a-b binding protein, chloroplastic / PSII 6.1 kDa protein / Photosystem II reaction center protein K / Photosystem II reaction center protein I / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II protein D1 / Cytochrome b559 subunit alpha / Photosystem II reaction center protein J / Oxygen-evolving enhancer protein 1, 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 / Photosystem II reaction center protein T / Ultraviolet-B-repressible protein / Photosystem II reaction center protein H / Photosystem II CP47 reaction center protein
Similarity search - Component
Biological speciesPisum sativum (garden pea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsGrinzato A / Albanese P / Zanotti G / Pagliano C
CitationJournal: Int J Mol Sci / Year: 2020
Title: High-Light versus Low-Light: Effects on Paired Photosystem II Supercomplex Structural Rearrangement in Pea Plants.
Authors: Alessandro Grinzato / Pascal Albanese / Roberto Marotta / Paolo Swuec / Guido Saracco / Martino Bolognesi / Giuseppe Zanotti / Cristina Pagliano /
Abstract: In plant thylakoid membranes Photosystem II (PSII) associates with a variable number of antenna proteins (LHCII) to form different types of supercomplexes (PSII-LHCII), whose organization is ...In plant thylakoid membranes Photosystem II (PSII) associates with a variable number of antenna proteins (LHCII) to form different types of supercomplexes (PSII-LHCII), whose organization is dynamically adjusted in response to light cues, with the CS more abundant in high-light and the CSM in low-light. Paired PSII-LHCII supercomplexes interacting at their stromal surface from adjacent thylakoid membranes were previously suggested to mediate stacking. Here, we present the cryo-electron microscopy maps of paired CS and CSM supercomplexes isolated from pea plants grown in high-light and low-light, respectively. These maps show a different rotational offset between the two supercomplexes in the pair, responsible for modifying their reciprocal interaction and energetic connectivity. This evidence reveals a different way by which paired PSII-LHCII supercomplexes can mediate stacking at diverse irradiances. Electrostatic stromal interactions between LHCII trimers almost completely overlapping in the paired CS can be the main determinant by which PSII-LHCII supercomplexes mediate stacking in plants grown in high-light, whereas the mutual interaction of stromal N-terminal loops of two facing Lhcb4 subunits in the paired CSM can fulfil this task in plants grown in low-light. The high-light induced accumulation of the Lhcb4.3 protein in PSII-LHCII supercomplexes has been previously reported. Our cryo-electron microscopy map at 3.8 Å resolution of the CS supercomplex isolated from plants grown in high-light suggests the presence of the Lhcb4.3 protein revealing peculiar structural features of this high-light-specific antenna important for photoprotection.
History
DepositionApr 15, 2020-
Header (metadata) releaseNov 25, 2020-
Map releaseNov 25, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.85
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.85
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yp7
  • Surface level: 0.85
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10865.png

Downloads & links

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Map

FileDownload / File: emd_10865.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPSIILHCII C2S2 supercomplex in high light condition
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.85 / Movie #1: 0.85
Minimum - Maximum-0.62992436 - 1.9226284
Average (Standard dev.)0.055471223 (±0.16558364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 374.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z374.000374.000374.000
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.6301.9230.055

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Supplemental data

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Sample components

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Entire : PSII-LHCII C2S2 supercomplex

EntireName: PSII-LHCII C2S2 supercomplex
Components
  • Complex: PSII-LHCII C2S2 supercomplex
    • Protein or peptide: Chlorophyll a-b binding protein 8, 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: 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: 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: Photosystem II reaction center protein Z
    • Protein or peptide: Light harvesting chlorophyll a/b-binding protein Lhcb4.3
    • Protein or peptide: Light harvesting chlorophyll a/b-binding protein Lhcb5, CP26
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-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: (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: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: FE (II) ION
  • Ligand: CHLORIDE IONChloride
  • Ligand: PHEOPHYTIN APheophytin
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: BICARBONATE IONBicarbonate
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: PSII-LHCII C2S2 supercomplex

SupramoleculeName: PSII-LHCII C2S2 supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Pisum sativum (garden pea)

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Macromolecule #1: Chlorophyll a-b binding protein 8, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 8, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 23.573473 KDa
Recombinant expressionOrganism: Pisum sativum (garden pea)
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 AWSYATNFVP G

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Macromolecule #2: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 36.972074 KDa
Recombinant expressionOrganism: Pisum sativum (garden pea)
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

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Macromolecule #3: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 55.659242 KDa
Recombinant expressionOrganism: Pisum sativum (garden pea)
SequenceString: GLPWYRVHTV VLNDPGRLLS VHIMHTALVA GWAGSMALYE LAVFDPSDPV LDPMWRQGMF VIPFMTRLGI TNSWGGWNIT GGTITNPGI WSYEGVAAAH IVFSGLCFLA AIWHWLYWDL EIFCDERTGK PSLDLPKIFG IHLFLAGVAC FGFGAFHVTG L FGPGIWVS ...String:
GLPWYRVHTV VLNDPGRLLS VHIMHTALVA GWAGSMALYE LAVFDPSDPV LDPMWRQGMF VIPFMTRLGI TNSWGGWNIT GGTITNPGI WSYEGVAAAH IVFSGLCFLA AIWHWLYWDL EIFCDERTGK PSLDLPKIFG IHLFLAGVAC FGFGAFHVTG L FGPGIWVS DPYGLTGRVQ SVNPAWGVDG FDPFVPGGIA SHHIAAGTLG ILAGLFHLSV RPPQRLYKGL RMGNIETVLS SS IAAVFFA AFVVAGTMWY GSATTPIELF GPTRYQWDQG YFQQEIYRRV SAGHVENQSL SEAWSKIPEK LAFYDYIGNN PAK GGLFRA GSMDNGDGIA VGWLGHPIFR DKEGRELFVR RMPTFFETFP VVLVDGDGIV RGDVPFRRAE SKYSVEQVGV IVEF YGGEL NGVTYSDPAT VKKYARRAQL GEIFELDRAT LKSDGVFRSS PRGWFTFGHA SFALLFFFGH IWHGARTLFR DLFAG IDPD LDAQVEFGAF QKLGDPTTR

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 49.275371 KDa
Recombinant expressionOrganism: Pisum sativum (garden pea)
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

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Macromolecule #5: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 38.220602 KDa
Recombinant expressionOrganism: Pisum sativum (garden pea)
SequenceString: NDLFDIMDDW LRRDRFVFVG WSGLLLFPCA YFAVGGWFTG TTFVTSWYTH GLASSYLEGC NFLTAAVSTP ANSLAHSLLL LWGPEAQGD LTRWCQLGGL WTFVALHGAF GLIGFMLRQF ELARSVQLRP YNAIAFSGPI AVFVSVFLIY PLGQSGWFFA P SFGVAAIF ...String:
NDLFDIMDDW LRRDRFVFVG WSGLLLFPCA YFAVGGWFTG TTFVTSWYTH GLASSYLEGC NFLTAAVSTP ANSLAHSLLL LWGPEAQGD LTRWCQLGGL WTFVALHGAF GLIGFMLRQF ELARSVQLRP YNAIAFSGPI AVFVSVFLIY PLGQSGWFFA P SFGVAAIF RFILFFQGFH NWTLNPFHMM GVAGVLGAAL LCAIHGATVE NTLFEDGDGA NTFRAFNPTQ AEETYSMVTA NR FWSQIFG VAFSNKRWLH FFMLFVPVTG LWMSALGVVG LALNLRAYDF VSQEIRAAED PEFETFYTKN ILLNEGIRAW MAT QDQPHE NLIFPEEVLP RGNAL

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Macromolecule #6: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 8.624707 KDa
Recombinant expressionOrganism: Pisum sativum (garden pea)
SequenceString:
RSFADIITSI RYWIIHSITI PSLFIAGWLF VSTGLAYDVF GSPRPNEYFT ETRQGIPLIT GRFDSLEQLD EFSRS

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Macromolecule #7: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.396035 KDa
Recombinant expressionOrganism: Pisum sativum (garden pea)
SequenceString:
FTVRWLAVHG LAVPTVFFLG SISAMQFIQR

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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
Recombinant expressionOrganism: Pisum sativum (garden pea)
SequenceString:
GPRRTAVGDL LKPLNSEYGK VAPGWGTTPL MGIAMALFAV FLSIILEIYN SSLLLDQISM

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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
Recombinant expressionOrganism: Pisum sativum (garden pea)
SequenceString:
MLTLKLFVYT IVIFFVSLFI FGFLSNDPGR NPGR

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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
Recombinant expressionOrganism: Pisum sativum (garden pea)
SequenceString:
GRIPLWIIGT VAGIVVIGLI GLFFYGSYSG LGSSL

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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
Recombinant expressionOrganism: Pisum sativum (garden pea)
SequenceString:
KLPEAYAFLN PIVDFMPVIP LLFFLLAFVW QAAVSFR

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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: 4.366904 KDa
Recombinant expressionOrganism: Pisum sativum (garden pea)
SequenceString:
TQSNPNEQNV ELNRTSLYWG LLLIFVLAVL FSNYFFN

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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
Recombinant expressionOrganism: Pisum sativum (garden pea)
SequenceString:
MEVNILAFIA TALFILVPTA FLLIIYVKTV SQS

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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
Recombinant expressionOrganism: Pisum sativum (garden pea)
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

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Macromolecule #15: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.692472 KDa
Recombinant expressionOrganism: Pisum sativum (garden pea)
SequenceString:
MEALVYTFLL VSTLGIIFFA IFFREPPKVP TK

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Macromolecule #16: Photosystem II reaction center protein W

MacromoleculeName: Photosystem II reaction center protein W / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 5.914629 KDa
Recombinant expressionOrganism: Pisum sativum (garden pea)
SequenceString:
LVDDRMSTEG TGLPFGLSNN LLGWILFGVF GLIWALYFIY ASGLDEDEES GLSL

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Macromolecule #17: Ultraviolet-B-repressible protein

MacromoleculeName: Ultraviolet-B-repressible protein / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.929627 KDa
Recombinant expressionOrganism: Pisum sativum (garden pea)
SequenceString:
ATVSPSLKNF LLSIVSGGVV VTAILGAVIG VSNFDPVKR

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Macromolecule #18: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 6.555742 KDa
Recombinant expressionOrganism: Pisum sativum (garden pea)
SequenceString:
MTIAFQLAVF ALIVTSSILL ISVPVVFASP DGWSSNKNVV FSGTSLWIGL VFLVGILNSL IS

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Macromolecule #19: Light harvesting chlorophyll a/b-binding protein Lhcb4.3

MacromoleculeName: Light harvesting chlorophyll a/b-binding protein Lhcb4.3
type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 24.460893 KDa
Recombinant expressionOrganism: Pisum sativum (garden pea)
SequenceString: GLVWFPGAQP PEWLDGTMIG DRGFDPLGFA KPAEYLQFDL DSLDQNLAKN LAGDVIGTRV EAGEVKPTPF QPYSEVFGIE RFRECELIH GRWAMLGALG ALAVEAFTGV AWQDAGKVEL VEGASYFGFS LPFSLTALIW IEVLVIGYIE FQRNAELDPE K RLYPGGKF ...String:
GLVWFPGAQP PEWLDGTMIG DRGFDPLGFA KPAEYLQFDL DSLDQNLAKN LAGDVIGTRV EAGEVKPTPF QPYSEVFGIE RFRECELIH GRWAMLGALG ALAVEAFTGV AWQDAGKVEL VEGASYFGFS LPFSLTALIW IEVLVIGYIE FQRNAELDPE K RLYPGGKF FDPLGLANDP EEKERLQLAE IKHSRLAMVV FLVFAIQAAV SGKGPIGFIA TFNQ

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Macromolecule #20: Light harvesting chlorophyll a/b-binding protein Lhcb5, CP26

MacromoleculeName: Light harvesting chlorophyll a/b-binding protein Lhcb5, CP26
type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 23.839139 KDa
Recombinant expressionOrganism: Pisum sativum (garden pea)
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

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Macromolecule #21: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 21 / Number of copies: 48 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

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Macromolecule #22: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 22 / Number of copies: 150 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #23: (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: 23 / Number of copies: 12 / 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 / Lutein

+
Macromolecule #24: (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: 24 / Number of copies: 8 / 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 / Violaxanthin

+
Macromolecule #25: (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: 25 / Number of copies: 7 / 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

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Macromolecule #26: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 26 / Number of copies: 26 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #27: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 27 / 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 #28: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 28 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #29: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 29 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #30: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 30 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A / Pheophytin

+
Macromolecule #31: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 31 / Number of copies: 22 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

+
Macromolecule #32: 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: 32 / 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 / Plastoquinone

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Macromolecule #33: 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: 33 / 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 #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 / Bicarbonate

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Macromolecule #35: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 35 / Number of copies: 10 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #36: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 36 / Number of copies: 14 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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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 / Heme B

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 BASE (4k x 4k) / #0 - Average electron dose: 40.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 BASE (4k x 4k) / #1 - Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5xnl

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27942
Image recording ID1

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