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- EMDB-6742: Structure of unstacked C2S2M2-type PSII-LHCII supercomplex from P... -

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Basic information

Entry
Database: EMDB / ID: EMD-6742
TitleStructure of unstacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
Map data
Sample
  • Complex: C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
    • Protein or peptide: x 23 types
  • Ligand: x 16 types
KeywordsPhotosystem II / PSII-LHCII / C2S2M2 / Supercomplex / MEMBRANE PROTEIN
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 / response to herbicide / photosystem II / 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 / metal ion binding
Similarity search - Function
Photosystem II 5kDa protein, chloroplastic / 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 5kDa protein, chloroplastic / 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 PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Photosystem II 5 kDa protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSII 6.1 kDa protein / Chlorophyll a-b binding protein, chloroplastic / 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 ...Photosystem II 5 kDa protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSII 6.1 kDa protein / Chlorophyll a-b binding protein, chloroplastic / 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 / Chlorophyll a-b binding protein, chloroplastic / 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: 3.2 Å
AuthorsSu XD / Ma J
Funding support China, 4 items
OrganizationGrant numberCountry
The Strategic Priority Research Program of CASXDB08020302 China
The Key Research Program of Frontier Sciences of CASQYZDB-SSW-SMC005 China
National 973 project grant2011CBA00900 China
National Natural Science Foundation of China31570724 and 31270793 China
CitationJournal: Science / Year: 2017
Title: Structure and assembly mechanism of plant CSM-type PSII-LHCII supercomplex.
Authors: Xiaodong Su / Jun Ma / Xuepeng Wei / Peng Cao / Dongjie Zhu / Wenrui Chang / Zhenfeng Liu / Xinzheng Zhang / Mei Li /
Abstract: In plants, the photosynthetic machinery photosystem II (PSII) consists of a core complex associated with variable numbers of light-harvesting complexes II (LHCIIs). The supercomplex, comprising a ...In plants, the photosynthetic machinery photosystem II (PSII) consists of a core complex associated with variable numbers of light-harvesting complexes II (LHCIIs). The supercomplex, comprising a dimeric core and two strongly bound and two moderately bound LHCIIs (CSM), is the dominant form in plants acclimated to limited light. Here we report cryo-electron microscopy structures of two forms of CSM (termed stacked and unstacked) from at 2.7- and 3.2-angstrom resolution, respectively. In each CSM, the moderately bound LHCII assembles specifically with a peripheral antenna complex CP24-CP29 heterodimer and the strongly bound LHCII, to establish a pigment network that facilitates light harvesting at the periphery and energy transfer into the core. The high mobility of peripheral antennae, including the moderately bound LHCII and CP24, provides insights into functional regulation of plant PSII.
History
DepositionMay 23, 2017-
Header (metadata) releaseSep 27, 2017-
Map releaseSep 27, 2017-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5xnm
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6742.png

Downloads & links

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Map

FileDownload / File: emd_6742.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026 / Movie #1: 0.026
Minimum - Maximum-0.057511434 - 0.11831094
Average (Standard dev.)0.00011920636 (±0.0067757596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-0.0580.1180.000

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Supplemental data

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Additional map: #1

Fileemd_6742_additional.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 : C2S2M2-type PSII-LHCII supercomplex from Pisum sativum

EntireName: C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
Components
  • Complex: C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
    • Protein or peptide: Chlorophyll a-b binding protein 8, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24
    • 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, PsbF
    • Protein or peptide: Photosystem II reaction center protein H
    • Protein or peptide: Photosystem II reaction center protein I, PsbI
    • 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: Light harvesting chlorophyll a/b-binding protein Lhcb4, CP29
    • Protein or peptide: Light harvesting chlorophyll a/b-binding protein Lhcb5, CP26
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: Photosystem II luminal extrinsic protein Tn, PsbTn
    • Protein or peptide: Photosystem II reaction center protein W, PSBW
    • Protein or peptide: Photosystem II reaction center protein X
    • Protein or peptide: Photosystem II reaction center protein Z
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: (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: BETA-CAROTENE
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: FE (II) ION
  • Ligand: PHEOPHYTIN A
  • 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: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: BICARBONATE ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: C2S2M2-type PSII-LHCII supercomplex from Pisum sativum

SupramoleculeName: C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#23
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: 10 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 24.952113 KDa
SequenceString: RKSATTKKVA SSGSPWYGPD RVKYLGPFSG ESPSYLTGEF PGDYGWDTAG LSADPETFSK NRELEVIHSR WAMLGALGCV FPELLSRNG VKFGEAVWFK AGSQIFSEGG LDYLGNPSLV HAQSILAIWA TQVILMGAVE GYRIAGGPLG EVVDPLYPGG S FDPLGLAD ...String:
RKSATTKKVA SSGSPWYGPD RVKYLGPFSG ESPSYLTGEF PGDYGWDTAG LSADPETFSK NRELEVIHSR WAMLGALGCV FPELLSRNG VKFGEAVWFK AGSQIFSEGG LDYLGNPSLV HAQSILAIWA TQVILMGAVE GYRIAGGPLG EVVDPLYPGG S FDPLGLAD DPEAFAELKV KELKNGRLAM FSMFGFFVQA IVTGKGPLEN LADHLSDPVN NNAWSYATNF VPGK

UniProtKB: Chlorophyll a-b binding protein 8, chloroplastic

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

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 26.54524 KDa
SequenceString: RKSANPLRDV VAMGTSKFTM GNDLWYGPDR VKYLGPFSAQ TPSYLTGEFP GDYGWDTAGL SADPEAFAKN RALEVIHGRW AMLGALGCI TPEVLQKWVR VDFKEPVWFK AGSQIFSEGG LDYLGNPNLV HAQSILAVLG FQIVLMGLVE GFRINGLPDV G EGNDLYPG ...String:
RKSANPLRDV VAMGTSKFTM GNDLWYGPDR VKYLGPFSAQ TPSYLTGEFP GDYGWDTAGL SADPEAFAKN RALEVIHGRW AMLGALGCI TPEVLQKWVR VDFKEPVWFK AGSQIFSEGG LDYLGNPNLV HAQSILAVLG FQIVLMGLVE GFRINGLPDV G EGNDLYPG GQYFDPLGLA DDPVTFAELK VKEIKNGRLA MFSMFGFFVQ AIVTGKGPLE NLLDHLDNPV ANNAWVYATK FV PGA

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #3: Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24

MacromoleculeName: Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24
type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 22.858957 KDa
SequenceString: AASAPKKSWI PGVSFGGNLV DPEWLDGSLP GDFGFDPLGL GKDPAFLKWY REAELIHGRW AMAAVLGIFV GQAWSGVPWF EAGADPNAI APFSFGTLLG TQLILMGWVE SKRWVDFFNP DSQSVEWATP WSKTAENFVN STGEQGYPGG KFFDPLSLAG T IENGVYIP ...String:
AASAPKKSWI PGVSFGGNLV DPEWLDGSLP GDFGFDPLGL GKDPAFLKWY REAELIHGRW AMAAVLGIFV GQAWSGVPWF EAGADPNAI APFSFGTLLG TQLILMGWVE SKRWVDFFNP DSQSVEWATP WSKTAENFVN STGEQGYPGG KFFDPLSLAG T IENGVYIP DTDKLERLKL AEIKHARLAM LAMLIFYFEA GQGKTPLGAL GL

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Macromolecule #4: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 38.14743 KDa
SequenceString: MTAILERRDS ENLWGRFCNW ITSTENRLYI GWFGVLMIPT LLTATSVFII AFIAAPPVDI DGIREPVSGS LLYGNNIISG AIIPTSAAI GLHFYPIWEA ASVDEWLYNG GPYELIVLHF LLGVACYMGR EWELSFRLGM RPWIAVAYSA PVAAATAVFL I YPIGQGSF ...String:
MTAILERRDS ENLWGRFCNW ITSTENRLYI GWFGVLMIPT LLTATSVFII AFIAAPPVDI DGIREPVSGS LLYGNNIISG AIIPTSAAI GLHFYPIWEA ASVDEWLYNG GPYELIVLHF LLGVACYMGR EWELSFRLGM RPWIAVAYSA PVAAATAVFL I YPIGQGSF SDGMPLGISG TFNFMIVFQA EHNILMHPFH MLGVAGVFGG SLFSAMHGSL VTSSLIRETT ENESANEGYR FG QEEETYN IVAAHGYFGR LIFQYASFNN SRSLHFFLAA WPVVGIWFTA LGISTMAFNL NGFNFNQSVV DSQGRVINTW ADI INRANL GMEVMHERNA HNFPLDLA

UniProtKB: Photosystem II protein D1

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Macromolecule #5: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 56.11784 KDa
SequenceString: MGLPWYRVHT VVLNDPGRLL SVHIMHTALV AGWAGSMALY ELAVFDPSDP VLDPMWRQGM FVIPFMTRLG ITNSWGGWNI TGGTITNPG IWSYEGVAAA HIVFSGLCFL AAIWHWLYWD LEIFCDERTG KPSLDLPKIF GIHLFLAGVA CFGFGAFHVT G LFGPGIWV ...String:
MGLPWYRVHT VVLNDPGRLL SVHIMHTALV AGWAGSMALY ELAVFDPSDP VLDPMWRQGM FVIPFMTRLG ITNSWGGWNI TGGTITNPG IWSYEGVAAA HIVFSGLCFL AAIWHWLYWD LEIFCDERTG KPSLDLPKIF GIHLFLAGVA CFGFGAFHVT G LFGPGIWV SDPYGLTGRV QSVNPAWGVD GFDPFVPGGI ASHHIAAGTL GILAGLFHLS VRPPQRLYKG LRMGNIETVL SS SIAAVFF AAFVVAGTMW YGSATTPIEL FGPTRYQWDQ GYFQQEIYRR VSAGHVENQS LSEAWSKIPE KLAFYDYIGN NPA KGGLFR AGSMDNGDGI AVGWLGHPIF RDKEGRELFV RRMPTFFETF PVVLVDGDGI VRGDVPFRRA ESKYSVEQVG VIVE FYGGE LNGVTYSDPA TVKKYARRAQ LGEIFELDRA TLKSDGVFRS SPRGWFTFGH ASFALLFFFG HIWHGARTLF RDLFA GIDP DLDAQVEFGA FQKLGDPTTR RGL

UniProtKB: Photosystem II CP47 reaction center protein

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Macromolecule #6: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 52.035629 KDa
SequenceString: MKTLYSLRRF YHVETLFNGT LALTGRDQET TGFAWWAGNA RLINLSGKLL GAHVAHAGLI VFWAGAMNLF EVAHFVPEKP MYEQGLILL PHLATLGWGV GPGGEVIDTF PYFVSGVLHL ISSAVLGFGG IYHALLGPET LEESFPFFGY VWKDRNKMTT I LGIHLILL ...String:
MKTLYSLRRF YHVETLFNGT LALTGRDQET TGFAWWAGNA RLINLSGKLL GAHVAHAGLI VFWAGAMNLF EVAHFVPEKP MYEQGLILL PHLATLGWGV GPGGEVIDTF PYFVSGVLHL ISSAVLGFGG IYHALLGPET LEESFPFFGY VWKDRNKMTT I LGIHLILL GIGSFLLVFK AFYFGGIYDT WAPGGGDVRK ITNFTLSPSI LFGYLLKSPF GGEGWIVSVD DLEDIIGGHV WL GSICILG GIWHILTKPF AWARRALVWS GEAYLSYSLG ALAVFGFIAC CFVWFNNTAY PSEFYGPTGP EASQAQAFTF LVR DQRLGA NVGSAQGPTG LGKYLMRSPT GEVIFGGETM RFWDLRAPWL EPLRGPNGLD LSRLKKDIQP WQERRSAEYM THAP LGSLN SVGGVATEIN AVNYVSPRSW LATSHFVLGF FLFVGHLWHA GRARAAAAGF EKGIDRDFEP VLSMTPLN

UniProtKB: Photosystem II CP43 reaction center protein

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Macromolecule #7: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 39.557199 KDa
SequenceString: MTIALGKFTK DQNDLFDIMD DWLRRDRFVF VGWSGLLLFP CAYFAVGGWF TGTTFVTSWY THGLASSYLE GCNFLTAAVS TPANSLAHS LLLLWGPEAQ GDLTRWCQLG GLWTFVALHG AFGLIGFMLR QFELARSVQL RPYNAIAFSG PIAVFVSVFL I YPLGQSGW ...String:
MTIALGKFTK DQNDLFDIMD DWLRRDRFVF VGWSGLLLFP CAYFAVGGWF TGTTFVTSWY THGLASSYLE GCNFLTAAVS TPANSLAHS LLLLWGPEAQ GDLTRWCQLG GLWTFVALHG AFGLIGFMLR QFELARSVQL RPYNAIAFSG PIAVFVSVFL I YPLGQSGW FFAPSFGVAA IFRFILFFQG FHNWTLNPFH MMGVAGVLGA ALLCAIHGAT VENTLFEDGD GANTFRAFNP TQ AEETYSM VTANRFWSQI FGVAFSNKRW LHFFMLFVPV TGLWMSALGV VGLALNLRAY DFVSQEIRAA EDPEFETFYT KNI LLNEGI RAWMATQDQP HENLIFPEEV LPRGNAL

UniProtKB: Photosystem II D2 protein

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Macromolecule #8: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 9.421555 KDa
SequenceString:
MSGSTGERSF ADIITSIRYW IIHSITIPSL FIAGWLFVST GLAYDVFGSP RPNEYFTETR QGIPLITGRF DSLEQLDEFS RSF

UniProtKB: Cytochrome b559 subunit alpha

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Macromolecule #9: Cytochrome b559 subunit beta, PsbF

MacromoleculeName: Cytochrome b559 subunit beta, PsbF / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 4.488324 KDa
SequenceString:
MTIDRTYPIF TVRWLAVHGL AVPTVFFLGS ISAMQFIQR

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Macromolecule #10: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 7.863094 KDa
SequenceString:
MATQTVENSS RSGPRRTAVG DLLKPLNSEY GKVAPGWGTT PLMGIAMALF AVFLSIILEI YNSSLLLDQI SMN

UniProtKB: Photosystem II reaction center protein H

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Macromolecule #11: Photosystem II reaction center protein I, PsbI

MacromoleculeName: Photosystem II reaction center protein I, PsbI / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 4.184918 KDa
SequenceString:
MLTLKLFVYT IVIFFVSLFI FGFLSNDPGR NPGREE

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Macromolecule #12: Photosystem II reaction center protein J

MacromoleculeName: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 4.116847 KDa
SequenceString:
MANTTGRIPL WIIGTVAGIV VIGLIGLFFY GSYSGLGSSL

UniProtKB: Photosystem II reaction center protein J

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Macromolecule #13: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 6.91229 KDa
SequenceString:
MLNIFSLVCI CINSALYSSS FFLGKLPEAY AFLNPIVDFM PVIPLLFFLL AFVWQAAVSF R

UniProtKB: Photosystem II reaction center protein K

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Macromolecule #14: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 4.4981 KDa
SequenceString:
MTQSNPNEQN VELNRTSLYW GLLLIFVLAV LFSNYFFN

UniProtKB: Photosystem II reaction center protein L

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Macromolecule #15: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.756513 KDa
SequenceString:
MEVNILAFIA TALFILVPTA FLLIIYVKTV SQSD

UniProtKB: Photosystem II reaction center protein M

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Macromolecule #16: Oxygen-evolving enhancer protein 1, chloroplastic

MacromoleculeName: Oxygen-evolving enhancer protein 1, chloroplastic / type: protein_or_peptide / ID: 16 / 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

+
Macromolecule #17: Light harvesting chlorophyll a/b-binding protein Lhcb4, CP29

MacromoleculeName: Light harvesting chlorophyll a/b-binding protein Lhcb4, CP29
type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 27.138688 KDa
SequenceString: KPSRSAPTTD RPLWFPGAKS PEYLDGSLVG DYGFDPFGLG KPAEYLQFDL DSLDQNLAKN LAGDVIGTRT EFEDVKSTPF QPYTEVFGL QRFRECELIH GRWAMLATLG ALTVEWLTGV TWQDAGKVEL VEGSTYLGQP LPFSITTLIW IEVLVIGYIE F QRNAELDS ...String:
KPSRSAPTTD RPLWFPGAKS PEYLDGSLVG DYGFDPFGLG KPAEYLQFDL DSLDQNLAKN LAGDVIGTRT EFEDVKSTPF QPYTEVFGL QRFRECELIH GRWAMLATLG ALTVEWLTGV TWQDAGKVEL VEGSTYLGQP LPFSITTLIW IEVLVIGYIE F QRNAELDS EKRLYPGGKF FDPLGLAADP EKKATLQLAE IKHARLAMVA FLGFAVQAAA TGKGPLNNWA THLSDPLHTT II DTFSSS

+
Macromolecule #18: Light harvesting chlorophyll a/b-binding protein Lhcb5, CP26

MacromoleculeName: Light harvesting chlorophyll a/b-binding protein Lhcb5, CP26
type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 26.541545 KDa
SequenceString: ALFSKKKAAP PKKAVVSPVD DELAKWYGPD RRIFLPEGLL DRSEIPAYLT GEVPGDYGYD PFGLSKKPDD FAKYQAYELI HGRWAMLGA AGFIIPEAFN KFGANCGPEA VWFKTGALLL DGNTLNYFGK NIPINLIFAV IAEVVLVGGA EYYRIINGLN L EDKLHPGG ...String:
ALFSKKKAAP PKKAVVSPVD DELAKWYGPD RRIFLPEGLL DRSEIPAYLT GEVPGDYGYD PFGLSKKPDD FAKYQAYELI HGRWAMLGA AGFIIPEAFN KFGANCGPEA VWFKTGALLL DGNTLNYFGK NIPINLIFAV IAEVVLVGGA EYYRIINGLN L EDKLHPGG PFDPLGLAKD PDQAAILKVK EIKNGRLAMF AMLGFFIQAY VTGEGPVENL AKHLSDPFAN NLLTVLAGSA ER APTL

+
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: 4.036859 KDa
SequenceString:
MEALVYTFLL VSTLGIIFFA IFFREPPKVP TKNTK

UniProtKB: Photosystem II reaction center protein T

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Macromolecule #20: Photosystem II luminal extrinsic protein Tn, PsbTn

MacromoleculeName: Photosystem II luminal extrinsic protein Tn, PsbTn / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 10.676572 KDa
SequenceString:
MASITMTASF LGTTVSKQPP THHLRRGVVM AKAMPETTTT TKEETSSKRR DLVFAVAAAA ACSVARIAMA EEPKRGTPEA KKKYAPVCV TMPSARICYK

+
Macromolecule #21: Photosystem II reaction center protein W, PSBW

MacromoleculeName: Photosystem II reaction center protein W, PSBW / type: protein_or_peptide / ID: 21 / 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

+
Macromolecule #22: Photosystem II reaction center protein X

MacromoleculeName: Photosystem II reaction center protein X / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 8.692072 KDa
SequenceString:
SIGRASSKSN GRFQVKASLK EKVVTGLTAA ALTAQMVIPD VAEAATVSPS LKNFLLSIVS GGVVVTAILG AVIGVSNFDP VKRGSQ

UniProtKB: Ultraviolet-B-repressible protein

+
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: 6.555742 KDa
SequenceString:
MTIAFQLAVF ALIVTSSILL ISVPVVFASP DGWSSNKNVV FSGTSLWIGL VFLVGILNSL IS

UniProtKB: Photosystem II reaction center protein Z

+
Macromolecule #24: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 24 / Number of copies: 98 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

+
Macromolecule #25: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 25 / Number of copies: 216 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #26: (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: 26 / Number of copies: 32 / 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 #27: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

MacromoleculeName: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 27 / Number of copies: 16 / 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 #28: (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: 28 / Number of copies: 16 / 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 #29: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 29 / Number of copies: 36 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #30: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 30 / Number of copies: 24 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #31: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 31 / Number of copies: 2 / Formula: OEX
Molecular weightTheoretical: 339.827 Da
Chemical component information

ChemComp-OEX:
CA-MN4-O5 CLUSTER

+
Macromolecule #32: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 32 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #33: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 33 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

+
Macromolecule #34: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

MacromoleculeName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
type: ligand / ID: 34 / Number of copies: 8 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

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

+
Macromolecule #35: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 35 / Number of copies: 14 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #36: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...

MacromoleculeName: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
type: ligand / ID: 36 / Number of copies: 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

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Macromolecule #37: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 37 / Number of copies: 10 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #38: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 38 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

+
Macromolecule #39: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 39 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.0 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50237
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

-
Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-5xnm:
Structure of unstacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum

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