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- PDB-8c29: Cryo-EM structure of photosystem II C2S2 supercomplex from Norway... -

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Basic information

Entry
Database: PDB / ID: 8c29
TitleCryo-EM structure of photosystem II C2S2 supercomplex from Norway spruce (Picea abies) at 2.8 Angstrom resolution
Components
  • (Chlorophyll a-b binding protein, ...) x 3
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 14
  • Oxygen-evolving enhancer protein 1, chloroplastic
  • PSII 6.1 kDa protein
KeywordsMEMBRANE PROTEIN / Membrane protein complex / Photosynthesis / Photosystem / Gymnosperm
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem I ...photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem I / photosystem II / response to herbicide / chlorophyll binding / photosynthetic electron transport in photosystem II / : / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis, light reaction / 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 PsbZ, reaction centre / Photosystem II CP47 reaction center protein / Photosystem II CP47 reaction center protein / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide ...Photosystem II 5kDa protein, chloroplastic / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II PsbZ, reaction centre / Photosystem II CP47 reaction center protein / Photosystem II CP47 reaction center protein / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II 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. / : / Chlorophyll A-B binding protein, plant and chromista / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Helix Hairpins / Roll / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL B / CHLOROPHYLL A / DIACYL GLYCEROL / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE ...1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL B / CHLOROPHYLL A / DIACYL GLYCEROL / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / ALPHA-LINOLENIC ACID / Chem-LUT / Chem-NEX / PALMITOLEIC ACID / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Chem-VIV / Chem-XAT / Photosystem II reaction center protein M / Photosystem II 5 kDa protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSII 6.1 kDa protein / 33 kDa subunit of oxygen evolving system of photosystem II / Uncharacterized protein / Photosystem II protein D1 / Chlorophyll a-b binding protein, chloroplastic / Photosystem II reaction center protein I / Photosystem II reaction center protein H / Photosystem II reaction center protein Z / Cytochrome b559 subunit beta / Photosystem II reaction center protein T / Photosystem II reaction center protein L / Cytochrome b559 subunit alpha / Photosystem II CP47 reaction center protein / Photosystem II D2 protein / Photosystem II reaction center protein K / Photosystem II reaction center protein Psb30 / Photosystem II CP43 reaction center protein
Similarity search - Component
Biological speciesPicea abies (Norway spruce)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.785 Å
AuthorsKopecny, D. / Semchonok, D.A. / Kouril, R.
Funding support Czech Republic, Germany, 9items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic21-05497S Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.1.01/0.0/0.0/16_019/0000827 Czech Republic
German Federal Ministry for Education and Research03Z22HN23 Germany
German Federal Ministry for Education and Research03Z22HI2 Germany
German Federal Ministry for Education and Research03COV04 Germany
German Research Foundation (DFG)391498659 Germany
German Research Foundation (DFG)RTG 2467 Germany
Ministry of Education, Youth and Sports of the Czech RepublicNo. CZ.02.1.01/0.0/0.0/18_046/0015974 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2018127 Czech Republic
CitationJournal: Nat Plants / Year: 2023
Title: Cryo-EM structure of a plant photosystem II supercomplex with light-harvesting protein Lhcb8 and α-tocopherol.
Authors: Monika Opatíková / Dmitry A Semchonok / David Kopečný / Petr Ilík / Pavel Pospíšil / Iva Ilíková / Pavel Roudnický / Sanja Ćavar Zeljković / Petr Tarkowski / Fotis L Kyrilis / ...Authors: Monika Opatíková / Dmitry A Semchonok / David Kopečný / Petr Ilík / Pavel Pospíšil / Iva Ilíková / Pavel Roudnický / Sanja Ćavar Zeljković / Petr Tarkowski / Fotis L Kyrilis / Farzad Hamdi / Panagiotis L Kastritis / Roman Kouřil /
Abstract: The heart of oxygenic photosynthesis is the water-splitting photosystem II (PSII), which forms supercomplexes with a variable amount of peripheral trimeric light-harvesting complexes (LHCII). Our ...The heart of oxygenic photosynthesis is the water-splitting photosystem II (PSII), which forms supercomplexes with a variable amount of peripheral trimeric light-harvesting complexes (LHCII). Our knowledge of the structure of green plant PSII supercomplex is based on findings obtained from several representatives of green algae and flowering plants; however, data from a non-flowering plant are currently missing. Here we report a cryo-electron microscopy structure of PSII supercomplex from spruce, a representative of non-flowering land plants, at 2.8 Å resolution. Compared with flowering plants, PSII supercomplex in spruce contains an additional Ycf12 subunit, Lhcb4 protein is replaced by Lhcb8, and trimeric LHCII is present as a homotrimer of Lhcb1. Unexpectedly, we have found α-tocopherol (α-Toc)/α-tocopherolquinone (α-TQ) at the boundary between the LHCII trimer and the inner antenna CP43. The molecule of α-Toc/α-TQ is located close to chlorophyll a614 of one of the Lhcb1 proteins and its chromanol/quinone head is exposed to the thylakoid lumen. The position of α-Toc in PSII supercomplex makes it an ideal candidate for the sensor of excessive light, as α-Toc can be oxidized to α-TQ by high-light-induced singlet oxygen at low lumenal pH. The molecule of α-TQ appears to shift slightly into the PSII supercomplex, which could trigger important structure-functional modifications in PSII supercomplex. Inspection of the previously reported cryo-electron microscopy maps of PSII supercomplexes indicates that α-Toc/α-TQ can be present at the same site also in PSII supercomplexes from flowering plants, but its identification in the previous studies has been hindered by insufficient resolution.
History
DepositionDec 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 30, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem II protein D1
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
G: Chlorophyll a-b binding protein, chloroplastic
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
N: Chlorophyll a-b binding protein, chloroplastic
O: Oxygen-evolving enhancer protein 1, chloroplastic
R: Chlorophyll a-b binding protein, chloroplastic
S: Chlorophyll a-b binding protein, chloroplastic
T: Photosystem II reaction center protein T
U: Photosystem II 5 kDa protein, chloroplastic
V: Photosystem II reaction center protein Ycf12
W: PSII 6.1 kDa protein
X: Photosystem II PsbX
Y: Chlorophyll a-b binding protein, chloroplastic
Z: Photosystem II reaction center protein Z
a: Photosystem II protein D1
b: Photosystem II CP47 reaction center protein
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
g: Chlorophyll a-b binding protein, chloroplastic
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
n: Chlorophyll a-b binding protein, chloroplastic
o: Oxygen-evolving enhancer protein 1, chloroplastic
r: Chlorophyll a-b binding protein, chloroplastic
s: Chlorophyll a-b binding protein, chloroplastic
t: Photosystem II reaction center protein T
u: Photosystem II 5 kDa protein, chloroplastic
v: Photosystem II reaction center protein Ycf12
w: PSII 6.1 kDa protein
x: Photosystem II PsbX
y: Chlorophyll a-b binding protein, chloroplastic
z: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,215,556404
Polymers945,03946
Non-polymers270,517358
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem II ... , 14 types, 28 molecules AaBbCcDdHhIiKkLlMmTtUuVvXxZz

#1: Protein Photosystem II protein D1 / PSII D1 protein / Photosystem II Q(B) protein


Mass: 38803.215 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbA / Source: (natural) Picea abies (Norway spruce) / References: UniProt: P50155, photosystem II
#2: Protein Photosystem II CP47 reaction center protein


Mass: 56375.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbB / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGX1
#3: Protein Photosystem II CP43 reaction center protein


Mass: 51785.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbC / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGZ0
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39483.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbD / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGX6, photosystem II
#8: Protein Photosystem II reaction center protein H / PSII-H


Mass: 7941.112 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbH / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGS7
#9: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 4184.984 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbI / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGS4
#10: Protein Photosystem II reaction center protein K


Mass: 6804.083 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbK / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGX8
#11: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4475.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbL / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGV2
#12: Protein/peptide Photosystem II reaction center protein M


Mass: 3952.636 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbM / Source: (natural) Picea abies (Norway spruce) / References: UniProt: A2CHR7
#16: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3962.781 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbTc / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGU2
#17: Protein Photosystem II 5 kDa protein, chloroplastic


Mass: 14189.462 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbTn / Source: (natural) Picea abies (Norway spruce) / References: UniProt: A9NJW3
#18: Protein/peptide Photosystem II reaction center protein Ycf12


Mass: 3490.290 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Psb30 / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGY5
#20: Protein Photosystem II PsbX


Mass: 12956.940 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbX / Source: (natural) Picea abies (Norway spruce) / References: UniProt: A9NTS2
#21: Protein Photosystem II reaction center protein Z


Mass: 6412.558 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbZ / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGT1

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Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf

#5: Protein Cytochrome b559 subunit alpha / PSII reaction center subunit V


Mass: 9478.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbE / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGW6
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4476.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbF / Source: (natural) Picea abies (Norway spruce) / References: UniProt: R4ZGT7

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Chlorophyll a-b binding protein, ... , 3 types, 10 molecules GNYgnyRrSs

#7: Protein
Chlorophyll a-b binding protein, chloroplastic


Mass: 29112.004 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: Lhcb1 / Source: (natural) Picea abies (Norway spruce) / References: UniProt: Q40771
#14: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 32767.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Lhcb4.3 / Source: (natural) Picea abies (Norway spruce) / References: UniProt: A9NKX0
#15: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 32287.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: CP26 / Source: (natural) Picea abies (Norway spruce) / References: UniProt: A9NKM0

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Protein , 2 types, 4 molecules OoWw

#13: Protein Oxygen-evolving enhancer protein 1, chloroplastic


Mass: 36089.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbO / Source: (natural) Picea abies (Norway spruce) / References: UniProt: A9NRV4
#19: Protein PSII 6.1 kDa protein


Mass: 15266.507 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PsbW / Source: (natural) Picea abies (Norway spruce) / References: UniProt: A9NLC2

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Sugars , 1 types, 4 molecules

#33: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 21 types, 634 molecules

#22: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#23: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 154 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#24: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#25: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56
#26: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H78O12S
#27: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C45H86O10
#28: Chemical
ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C39H77O8P
#29: Chemical
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 9


Mass: 749.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C53H80O2
#30: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#31: Chemical...
ChemComp-LNL / ALPHA-LINOLENIC ACID


Mass: 278.430 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C18H30O2
#32: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30O2
#34: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#35: Chemical ChemComp-VIV / (2R)-2,5,7,8-TETRAMETHYL-2-[(4R,8R)-4,8,12-TRIMETHYLTRIDECYL]CHROMAN-6-OL


Mass: 430.706 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H50O2
#36: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3
#37: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H76O5
#38: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#39: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#40: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN


Mass: 568.871 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C40H56O2
#41: Chemical
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 / (3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL / 9'-CIS-NEOXANTHIN


Mass: 600.870 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C40H56O4
#42: Chemical
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


Mass: 600.870 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H56O4
#43: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1The C2S2-type PSII-LHCII supercomplexCOMPLEX#1-#210NATURAL
2Photosystem II core complex (C2)COMPLEX#1-#6, #8-#13, #16-#211NATURAL
3Photosystem II light-harvesting complexCOMPLEX#7, #14-#151NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Picea abies (Norway spruce)3329
32Picea abies (Norway spruce)3329
43Picea abies (Norway spruce)3329
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPESC8H18N2O4S1
20.008 %n-dodecyl alpha-D-maltosideC24H46O111
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 3 mg of chlorophylls/ml
Specimen supportDetails: PELCO easiGlow, 15 mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingElectron dose: 120 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2392
Image scansWidth: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1Scipion3particle selection
2Xmipp3particle selection
3EPU2image acquisition
5CTFFIND4.1CTF correction
8Coot0.9.8model fitting
10cryoSPARC3initial Euler assignmentab-initio
11cryoSPARC3final Euler assignment
12RELION3.1classification
13cryoSPARC33D reconstruction
14PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 202251
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.785 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60956 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00674166
ELECTRON MICROSCOPYf_angle_d0.636103333
ELECTRON MICROSCOPYf_dihedral_angle_d14.9715560
ELECTRON MICROSCOPYf_chiral_restr0.0469284
ELECTRON MICROSCOPYf_plane_restr0.00514262

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