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- EMDB-3491: Cryo-EM structure of the PSII supercomplex from Arabidopsis thaliana -

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Basic information

Entry
Database: EMDB / ID: EMD-3491
TitleCryo-EM structure of the PSII supercomplex from Arabidopsis thaliana
Map data
Sample
  • Complex: C2S2M2 supercomplex of Photosystem II
    • Protein or peptide: x 20 types
  • Ligand: x 5 types
Keywordsphotosynthesis / photosystem II supercomplex / single particle analysis
Function / homology
Function and homology information


photoinhibition / photosystem II antenna complex / PSII associated light-harvesting complex II / nonphotochemical quenching / chloroplast stromal thylakoid / plastid thylakoid membrane / thylakoid lumen / plastoglobule / thylakoid membrane / chloroplast thylakoid ...photoinhibition / photosystem II antenna complex / PSII associated light-harvesting complex II / nonphotochemical quenching / chloroplast stromal thylakoid / plastid thylakoid membrane / thylakoid lumen / plastoglobule / thylakoid membrane / chloroplast thylakoid / thylakoid / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem II oxygen evolving complex / apoplast / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / chloroplast envelope / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem I / response to herbicide / photosystem II / poly(U) RNA binding / plastid / chloroplast stroma / chlorophyll binding / photosynthetic electron transport in photosystem II / phosphate ion binding / photosynthesis, light reaction / chloroplast thylakoid membrane / : / photosynthesis / chloroplast / electron transfer activity / protein stabilization / iron ion binding / protein domain specific binding / mRNA binding / heme binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / 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 PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / 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
Chlorophyll a-b binding protein 1, chloroplastic / Oxygen-evolving enhancer protein 1-1, chloroplastic / Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Cytochrome b559 subunit alpha / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II reaction center protein Z / Photosystem II reaction center protein L ...Chlorophyll a-b binding protein 1, chloroplastic / Oxygen-evolving enhancer protein 1-1, chloroplastic / Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Cytochrome b559 subunit alpha / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II reaction center protein Z / Photosystem II reaction center protein L / Photosystem II reaction center protein T / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein M / Photosystem II protein D1 / Chlorophyll a-b binding protein CP29.1, chloroplastic / Photosystem II reaction center W protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Expressed protein / Chlorophyll a-b binding protein CP26, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.3 Å
Authorsvan Bezouwen LS / Caffarri S
CitationJournal: Nat Plants / Year: 2017
Title: Subunit and chlorophyll organization of the plant photosystem II supercomplex.
Authors: Laura S van Bezouwen / Stefano Caffarri / Ravindra S Kale / Roman Kouřil / Andy-Mark W H Thunnissen / Gert T Oostergetel / Egbert J Boekema /
Abstract: Photosystem II (PSII) is a light-driven protein, involved in the primary reactions of photosynthesis. In plant photosynthetic membranes PSII forms large multisubunit supercomplexes, containing a ...Photosystem II (PSII) is a light-driven protein, involved in the primary reactions of photosynthesis. In plant photosynthetic membranes PSII forms large multisubunit supercomplexes, containing a dimeric core and up to four light-harvesting complexes (LHCs), which act as antenna proteins. Here we solved a three-dimensional (3D) structure of the CSM supercomplex from Arabidopsis thaliana using cryo-transmission electron microscopy (cryo-EM) and single-particle analysis at an overall resolution of 5.3 Å. Using a combination of homology modelling and restrained refinement against the cryo-EM map, it was possible to model atomic structures for all antenna complexes and almost all core subunits. We located all 35 chlorophylls of the core region based on the cyanobacterial PSII structure, whose positioning is highly conserved, as well as all the chlorophylls of the LHCII S and M trimers. A total of 13 and 9 chlorophylls were identified in CP26 and CP24, respectively. Energy flow from LHC complexes to the PSII reaction centre is proposed to follow preferential pathways: CP26 and CP29 directly transfer to the core using several routes for efficient transfer; the S trimer is directly connected to CP43 and the M trimer can efficiently transfer energy to the core through CP29 and the S trimer.
History
DepositionNov 13, 2016-
Header (metadata) releaseJun 21, 2017-
Map releaseJun 21, 2017-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5mdx
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3491.png

Downloads & links

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Map

FileDownload / File: emd_3491.map.gz / Format: CCP4 / Size: 391 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 468 pix.
= 517.14 Å		1.11 Å/pix.
x 468 pix.
= 517.14 Å		1.11 Å/pix.
x 468 pix.
= 517.14 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.105 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.06522754 - 0.16893475
Average (Standard dev.)0.00003392252 (±0.006831716)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions468468468
Spacing468468468
CellA=B=C: 517.14 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1051.1051.105
M x/y/z468468468
origin x/y/z0.0000.0000.000
length x/y/z517.140517.140517.140
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS468468468
D min/max/mean-0.0650.1690.000

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Supplemental data

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Half map: #1

Fileemd_3491_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_3491_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 : C2S2M2 supercomplex of Photosystem II

EntireName: C2S2M2 supercomplex of Photosystem II
Components
  • Complex: C2S2M2 supercomplex of Photosystem II
    • 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
    • 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 1-1, chloroplastic
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: Photosystem II reaction center W protein, chloroplastic
    • Protein or peptide: Photosystem II reaction center protein X
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: Chlorophyll a-b binding protein CP29.1, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein CP26, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein 1, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Ligand: FE (II) ION
  • Ligand: CHLOROPHYLL A
  • Ligand: PHEOPHYTIN A
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CHLOROPHYLL B

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Supramolecule #1: C2S2M2 supercomplex of Photosystem II

SupramoleculeName: C2S2M2 supercomplex of Photosystem II / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 38.003234 KDa
SequenceString: TAILERRESE SLWGRFCNWI TSTENRLYIG WFGVLMIPTL LTATSVFIIA FIAAPPVDID GIREPVSGSL LYGNNIISGA IIPTSAAIG LHFYPIWEAA SVDEWLYNGG PYELIVLHFL LGVACYMGRE WELSFRLGMR PWIAVAYSAP VAAATAVFLI Y PIGQGSFS ...String:
TAILERRESE SLWGRFCNWI TSTENRLYIG WFGVLMIPTL LTATSVFIIA FIAAPPVDID GIREPVSGSL LYGNNIISGA IIPTSAAIG LHFYPIWEAA SVDEWLYNGG PYELIVLHFL LGVACYMGRE WELSFRLGMR PWIAVAYSAP VAAATAVFLI Y PIGQGSFS DGMPLGISGT FNFMIVFQAE HNILMHPFHM LGVAGVFGGS LFSAMHGSLV TSSLIRETTE NESANEGYRF GQ EEETYNI VAAHGYFGRL IFQYASFNNS RSLHFFLAAW PVVGIWFTAL GISTMAFNLN GFNFNQSVVD SQGRVINTWA DII NRANLG MEVMHERNAH NFPLDLA

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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 55.960625 KDa
SequenceString: GLPWYRVHTV VLNDPGRLLA VHIMHTALVA GWAGSMALYE LAVFDPSDPV LDPMWRQGMF VIPFMTRLGI TNSWGGWNIT GGTITNPGL WSYEGVAGAH IVFSGLCFLA AIWHWVYWDL EIFCDERTGK PSLDLPKIFG IHLFLSGVAC FGFGAFHVTG L YGPGIWVS ...String:
GLPWYRVHTV VLNDPGRLLA VHIMHTALVA GWAGSMALYE LAVFDPSDPV LDPMWRQGMF VIPFMTRLGI TNSWGGWNIT GGTITNPGL WSYEGVAGAH IVFSGLCFLA AIWHWVYWDL EIFCDERTGK PSLDLPKIFG IHLFLSGVAC FGFGAFHVTG L YGPGIWVS DPYGLTGKVQ PVNPAWGVEG FDPFVPGGIA SHHIAAGTLG ILAGLFHLSV RPPQRLYKGL RMGNIETVLS SS IAAVFFA AFVVAGTMWY GSATTPIELF GPTRYQWDQG YFQQEIYRRV SAGLAENQSL SEAWAKIPEK LAFYDYIGNN PAK GGLFRA GSMDNGDGIA VGWLGHPVFR NKEGRELFVR RMPTFFETFP VVLVDGDGIV RADVPFRRAE SKYSVEQVGV TVEF YGGEL NGVSYSDPAT VKKYARRAQL GEIFELDRAT LKSDGVFRSS PRGWFTFGHA SFALLFFFGH IWHGARTLFR DVFAG IDPD LDAQVEFGAF QKLGDPTTKR QAV

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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 50.086324 KDa
SequenceString: TLFNGTLALA GRDQETTGFA WWAGNARLIN LSGKLLGAHV AHAGLIVFWA GAMNLFEVAH FVPEKPMYEQ GLILLPHLAT LGWGVGPGG EVIDTFPYFV SGVLHLISSA VLGFGGIYHA LLGPETLEES FPFFGYVWKD RNKMTTILGI HLILLGVGAF L LVFKALYF ...String:
TLFNGTLALA GRDQETTGFA WWAGNARLIN LSGKLLGAHV AHAGLIVFWA GAMNLFEVAH FVPEKPMYEQ GLILLPHLAT LGWGVGPGG EVIDTFPYFV SGVLHLISSA VLGFGGIYHA LLGPETLEES FPFFGYVWKD RNKMTTILGI HLILLGVGAF L LVFKALYF GGVYDTWAPG GGDVRKITNL TLSPSVIFGY LLKSPFGGEG WIVSVDDLED IIGGHVWLGS ICIFGGIWHI LT KPFAWAR RALVWSGEAY LSYSLAALSV CGFIACCFVW FNNTAYPSEF YGPTGPEASQ AQAFTFLVRD QRLGANVGSA QGP TGLGKY LMRSPTGEVI FGGETMRFWD LRAPWLEPLR GPNGLDLSRL KKDIQPWQER RSAEYMTHAP LGSLNSVGGV ATEI NAVNY VSPRSWLSTS HFVLGFFLFV GHLWHAGRAR AAAAGFEKGI DRDFEPVLSM TPLN

UniProtKB: Photosystem II CP43 reaction center protein

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Macromolecule #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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 39.444082 KDa
SequenceString: TIALGKFTKD EKDLFDIMDD WLRRDRFVFV GWSGLLLFPC AYFALGGWFT GTTFVTSWYT HGLASSYLEG CNFLTAAVST PANSLAHSL LLLWGPEAQG DFTRWCQLGG LWAFVALHGA FALIGFMLRQ FELARSVQLR PYNAIAFSGP IAVFVSVFLI Y PLGQSGWF ...String:
TIALGKFTKD EKDLFDIMDD WLRRDRFVFV GWSGLLLFPC AYFALGGWFT GTTFVTSWYT HGLASSYLEG CNFLTAAVST PANSLAHSL LLLWGPEAQG DFTRWCQLGG LWAFVALHGA FALIGFMLRQ FELARSVQLR PYNAIAFSGP IAVFVSVFLI Y PLGQSGWF FAPSFGVAAI FRFILFFQGF HNWTLNPFHM MGVAGVLGAA LLCAIHGATV ENTLFEDGDG ANTFRAFNPT QA EETYSMV TANRFWSQIF GVAFSNKRWL HFFMLFVPVT GLWMSALGVV GLALNLRAYD FVSQEIRAAE DPEFETFYTK NIL LNEGIR AWMAAQDQPH ENLIFPEEVL PRGNAL

UniProtKB: Photosystem II D2 protein

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Macromolecule #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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 9.393501 KDa
SequenceString:
MSGSTGERSF ADIITSIRYW VIHSITIPSL FIAGWLFVST GLAYDVFGSP RPNEYFTESR QGIPLITGRF DSLEQLDEFS RSF

UniProtKB: Cytochrome b559 subunit alpha

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Macromolecule #6: Cytochrome b559 subunit beta (PsbF)

MacromoleculeName: Cytochrome b559 subunit beta (PsbF) / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 4.428228 KDa
SequenceString:
MTIDRTYPIF TVRWLAVHGL AVPTVSFLGS ISAMQFIQR

UniProtKB: Cytochrome b559 subunit beta

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Macromolecule #7: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 7.575691 KDa
SequenceString:
ATQTVEDSSR SGPRSTTVGK LLKPLNSEYG KVAPGWGTTP LMGVAMALFA VFLSIILEIY NSSVLLDGIS VN

UniProtKB: Photosystem II reaction center protein H

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Macromolecule #8: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 4.170891 KDa
SequenceString:
MLTLKLFVYT VVIFFVSLFI FGFLSNDPGR NPGREE

UniProtKB: Photosystem II reaction center protein I

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Macromolecule #9: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 4.239112 KDa
SequenceString:
KLPEAYAFLN PIVDVMPVIP LFFLLLAFVW QAAVSFR

UniProtKB: Photosystem II reaction center protein K

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Macromolecule #10: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 4.471075 KDa
SequenceString:
MTQSNPNEQS VELNRTSLYW GLLLIFVLAV LFSNYFFN

UniProtKB: Photosystem II reaction center protein L

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Macromolecule #11: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 3.783538 KDa
SequenceString:
MEVNILAFIA TALFILVPTA FLLIIYVKTV SQND

UniProtKB: Photosystem II reaction center protein M

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Macromolecule #12: Oxygen-evolving enhancer protein 1-1, chloroplastic

MacromoleculeName: Oxygen-evolving enhancer protein 1-1, chloroplastic / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 26.594639 KDa
SequenceString: EGAPKRLTYD EIQSKTYMEV KGTGTANQCP TIDGGSETFS FKPGKYAGKK FCFEPTSFTV KADSVSKNAP PEFQNTKLMT RLTYTLDEI EGPFEVASDG SVNFKEEDGI DYAAVTVQLP GGERVPFLFT VKQLDASGKP DSFTGKFLVP SYRGSSFLDP K GRGGSTGY ...String:
EGAPKRLTYD EIQSKTYMEV KGTGTANQCP TIDGGSETFS FKPGKYAGKK FCFEPTSFTV KADSVSKNAP PEFQNTKLMT RLTYTLDEI EGPFEVASDG SVNFKEEDGI DYAAVTVQLP GGERVPFLFT VKQLDASGKP DSFTGKFLVP SYRGSSFLDP K GRGGSTGY DNAVALPAGG RGDEEELVKE NVKNTAASVG EITLKVTKSK PETGEVIGVF ESLQPSDTDL GAKVPKDVKI QG VWYGQLE

UniProtKB: Oxygen-evolving enhancer protein 1-1, chloroplastic

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Macromolecule #13: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 3.825642 KDa
SequenceString:
MEALVYTFLL VSTLGIIFFA IFFREPPKIS TKK

UniProtKB: Photosystem II reaction center protein T

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Macromolecule #14: Photosystem II reaction center W protein, chloroplastic

MacromoleculeName: Photosystem II reaction center W protein, chloroplastic
type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 6.036749 KDa
SequenceString:
LVDERMSTEG TGLPFGLSNN LLGWILFGVF GLIWTFFFVY TSSLEEDEES GLSL

UniProtKB: Photosystem II reaction center W protein, chloroplastic

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Macromolecule #15: Photosystem II reaction center protein X

MacromoleculeName: Photosystem II reaction center protein X / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 11.826013 KDa
SequenceString:
MASTSAMSLV TPLNQTRSSP FLKPLPLKPS KALVATGGRA QRLQVKALKM DKALTGISAA ALTASMVIPE IAEAAGSGIS PSLKNFLLS IASGGLVLTV IIGVVVGVSN FDPVKRT

UniProtKB: Expressed protein

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Macromolecule #16: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 6.569768 KDa
SequenceString:
MTIAFQLAVF ALIITSSILL ISVPVVFASP DGWSSNKNVV FSGTSLWIGL VFLVGILNSL IS

UniProtKB: Photosystem II reaction center protein Z

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Macromolecule #17: Chlorophyll a-b binding protein CP29.1, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein CP29.1, chloroplastic / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 27.302855 KDa
SequenceString: AAPKKSAKKT VTTDRPLWYP GAISPDWLDG SLVGDYGFDP FGLGKPAEYL QFDIDSLDQN LAKNLAGDVI GTRTEAADAK STPFQPYSE VFGIQRFREC ELIHGRWAML ATLGALSVEW LTGVTWQDAG KVELVDGSSY LGQPLPFSIS TLIWIEVLVI G YIEFQRNA ...String:
AAPKKSAKKT VTTDRPLWYP GAISPDWLDG SLVGDYGFDP FGLGKPAEYL QFDIDSLDQN LAKNLAGDVI GTRTEAADAK STPFQPYSE VFGIQRFREC ELIHGRWAML ATLGALSVEW LTGVTWQDAG KVELVDGSSY LGQPLPFSIS TLIWIEVLVI G YIEFQRNA ELDSEKRLYP GGKFFDPLGL AADPEKTAQL QLAEIKHARL AMVAFLGFAV QAAATGKGPL NNWATHLSDP LH TTIIDTF SSS

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

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Macromolecule #18: Chlorophyll a-b binding protein CP26, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein CP26, chloroplastic / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 25.232754 KDa
SequenceString: SKAVSETSDE LAKWYGPDRR IFLPDGLLDR SEIPEYLNGE VAGDYGYDPF GLGKKPENFA KYQAFELIHA RWAMLGAAGF IIPEALNKY GANCGPEAVW FKTGALLLDG NTLNYFGKNI PINLVLAVVA EVVLLGGAEY YRITNGLDFE DKLHPGGPFD P LGLAKDPE ...String:
SKAVSETSDE LAKWYGPDRR IFLPDGLLDR SEIPEYLNGE VAGDYGYDPF GLGKKPENFA KYQAFELIHA RWAMLGAAGF IIPEALNKY GANCGPEAVW FKTGALLLDG NTLNYFGKNI PINLVLAVVA EVVLLGGAEY YRITNGLDFE DKLHPGGPFD P LGLAKDPE QGALLKVKEI KNGRLAMFAM LGFFIQAYVT GEGPVENLAK HLSDPFGNNL LTVIAGTAER APTL

UniProtKB: Chlorophyll a-b binding protein CP26, chloroplastic

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Macromolecule #19: Chlorophyll a-b binding protein 1, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 1, chloroplastic / type: protein_or_peptide / ID: 19 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 23.97191 KDa
SequenceString: GPSGSPWYGS DRVKYLGPFS GESPSYLTGE FPGDYGWDTA GLSADPETFA RNRELEVIHS RWAMLGALGC VFPELLARNG VKFGEAVWF KAGSQIFSDG GLDYLGNPSL VHAQSILAIW ATQVILMGAV EGYRVAGNGP LGEAEDLLYP GGSFDPLGLA T DPEAFAEL ...String:
GPSGSPWYGS DRVKYLGPFS GESPSYLTGE FPGDYGWDTA GLSADPETFA RNRELEVIHS RWAMLGALGC VFPELLARNG VKFGEAVWF KAGSQIFSDG GLDYLGNPSL VHAQSILAIW ATQVILMGAV EGYRVAGNGP LGEAEDLLYP GGSFDPLGLA T DPEAFAEL KVKELKNGRL AMFSMFGFFV QAIVTGKGPI ENLADHLADP VNNNAWAFAT NFVPGK

UniProtKB: Chlorophyll a-b binding protein 1, chloroplastic

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Macromolecule #20: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 23.014051 KDa
SequenceString: AAAAQPKKSW IPAVKGGGNF LDPEWLDGSL PGDFGFDPLG LGKDPAFLKW YREAELIHGR WAMAAVLGIF VGQAWSGVAW FEAGAQPDA IAPFSFGSLL GTQLLLMGWV ESKRWVDFFN PDSQSVEWAT PWSKTAENFA NYTGDQGYPG GRFFDPLGLA G KNRDGVYE ...String:
AAAAQPKKSW IPAVKGGGNF LDPEWLDGSL PGDFGFDPLG LGKDPAFLKW YREAELIHGR WAMAAVLGIF VGQAWSGVAW FEAGAQPDA IAPFSFGSLL GTQLLLMGWV ESKRWVDFFN PDSQSVEWAT PWSKTAENFA NYTGDQGYPG GRFFDPLGLA G KNRDGVYE PDFEKLERLK LAEIKHSRLA MVAMLIFYFE AGQGKTPLGA LG

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #21: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 21 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #22: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 22 / Number of copies: 212 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #23: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 23 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #24: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 24 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #25: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 25 / Number of copies: 96 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Microscope had a Cs corrector
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-7 / Number grids imaged: 3 / Number real images: 5198 / Average exposure time: 1.0 sec. / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: The RANSAC method is used (Vargas 2014)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 23434
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.3)
Final 3D classificationSoftware - Name: RELION (ver. 1.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsInitial fitting of the subunits in the cryo-EM map was performed by rigid body real space refinement, using as templates the high resolution crystal structures of Thermosynechococcus vulcanus PSII (PDB code 3WU2), pea LHC-II (PDB code 2BHW for the S- and M-trimers, and spinach CP29 (PDB code 3PL9) for CP29, CP26 and CP24. Local fitting and adjustment of the subunits in the cryo-EM maps was performed using manual rebuilding and restrained real space refinement as explained in the primary reference. Due to large differences in local resolution of the cryo-EM map, refinement of the PSII core, the S-trimer with CP26/CP29 and the M-trimer with CP24 was performed separately in excised parts of the cryo-EM map. The core was refined at 4.5 angstrom, the S-trimer+CP26+CP29 at 5.5 angstrom and the M-trimer+CP24 at 6.5 angstrom. Core: chains A,B,C,D,E,F,H,I,J,K,L,M,O,T,W,X,Z and a,b,c,d,e,f,h,i,j,k,l,m,o,t,w,x,z. S-trimer+CP26+CP29: chains G,N,Y,S,R and g,n,y,s,r. M-trimer+CP24: chains 1,2,3,4 and 5,6,7,8.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-5mdx:
Cryo-EM structure of the PSII supercomplex from Arabidopsis thaliana

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