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Entry
Database: PDB / ID: 8iwh
TitleStructure and characteristics of a photosystem II supercomplex containing monomeric LHCX and dimeric FCPII antennae from the diatom Thalassiosira pseudonana
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Fucoxanthin chlorophyll a/c ...) x 4
  • (Photosystem II ...) x 18
  • Cytochrome c-550
  • Fucoxanthin chl a/c protein, lhca clade
  • Fucoxanthin-chlorophyll a-c binding protein, plastid
  • Oxygen-evolving enhancer protein 1
  • PS II complex 12 kDa extrinsic protein
KeywordsPHOTOSYNTHESIS / PSII supercomplex / LHCX / FCP
Function / homology
Function and homology information


light-harvesting complex / cytochrome c-heme linkage / photosynthesis, light harvesting in photosystem I / photosystem II assembly / photosystem II stabilization / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / thylakoid / photosynthetic electron transport chain ...light-harvesting complex / cytochrome c-heme linkage / photosynthesis, light harvesting in photosystem I / photosystem II assembly / photosystem II stabilization / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / thylakoid / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / plastid / extrinsic component of membrane / photosynthetic electron transport in photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / response to light stimulus / photosynthesis / respiratory electron transport chain / chloroplast / electron transfer activity / protein stabilization / iron ion binding / heme binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Photosystem II Psb31 protein / Photosystem II Psb31 protein / PsbQ-like domain superfamily / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ ...Photosystem II Psb31 protein / Photosystem II Psb31 protein / PsbQ-like domain superfamily / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II PsbM superfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbM / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Chem-A86 / BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-ET4 / : / PROTOPORPHYRIN IX CONTAINING FE / Chlorophyll c1 ...Chem-A86 / BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-ET4 / : / PROTOPORPHYRIN IX CONTAINING FE / Chlorophyll c1 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Cytochrome c-550 / Photosystem II reaction center X protein / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein T / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II D2 protein / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein Ycf12 / Photosystem II reaction center protein Z / Photosystem II reaction center protein J / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Cytochrome b559 subunit alpha / Photosystem II reaction center protein I / Photosystem II protein D1 / Fucoxanthin chlorophyll a/c protein-LI818 clade / Uncharacterized protein / Fucoxanthin chl a/c protein, lhca clade / Fucoxanthin-chlorophyll a-c binding protein, plastid / PS II complex 12 kDa extrinsic protein / Fucoxanthin chlorophyll a/c protein 6 / Fucoxanthin chlorophyll a/c light-harvesting protein, major type / Photosystem II reaction center M protein, plastid / Oxygen-evolving enhancer protein 1 / PSII 6.1 kDa protein / Photosystem II Psb31 protein domain-containing protein / Fucoxanthin chlorophyll a/c protein 5
Similarity search - Component
Biological speciesThalassiosira pseudonana (Diatom)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsFeng, Y. / Li, Z.H. / Wang, W.D. / Shen, J.R.
Funding support China, 9items
OrganizationGrant numberCountry
Chinese Academy of Sciences2019YFA0906300 China
Chinese Academy of Sciences2021YFA1300403 China
Chinese Academy of SciencesXDA26050402 China
Chinese Academy of SciencesXDB17000000 China
Chinese Academy of Sciences2020081 China
Chinese Academy of SciencesJCTD-2020-06 China
Chinese Academy of SciencesYSBR-004 China
Chinese Academy of Sciences31970260 China
Chinese Academy of Sciences32222007 China
CitationJournal: Sci Adv / Year: 2023
Title: Structure of a diatom photosystem II supercomplex containing a member of Lhcx family and dimeric FCPII.
Authors: Yue Feng / Zhenhua Li / Xiaoyi Li / Lili Shen / Xueyang Liu / Cuicui Zhou / Jinyang Zhang / Min Sang / Guangye Han / Wenqiang Yang / Tingyun Kuang / Wenda Wang / Jian-Ren Shen /
Abstract: Diatoms rely on fucoxanthin chlorophyll -binding proteins (FCPs) for their great success in oceans, which have a great diversity in their pigment, protein compositions, and subunit organizations. We ...Diatoms rely on fucoxanthin chlorophyll -binding proteins (FCPs) for their great success in oceans, which have a great diversity in their pigment, protein compositions, and subunit organizations. We report a unique structure of photosystem II (PSII)-FCPII supercomplex from at 2.68-Å resolution by cryo-electron microscopy. FCPIIs within this PSII-FCPII supercomplex exist in dimers and monomers, and a homodimer and a heterodimer were found to bind to a PSII core. The FCPII homodimer is formed by Lhcf7 and associates with PSII through an Lhcx family antenna Lhcx6_1, whereas the heterodimer is formed by Lhcf6 and Lhcf11 and connects to the core together with an Lhcf5 monomer through Lhca2 monomer. An extended pigment network consisting of diatoxanthins, diadinoxanthins, fucoxanthins, and chlorophylls is revealed, which functions in efficient light harvesting, energy transfer, and dissipation. These results provide a structural basis for revealing the energy transfer and dissipation mechanisms and also for the structural diversity of FCP antennas in diatoms.
History
DepositionMar 30, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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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
c: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
d: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
e: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
f: Cytochrome b559 subunit beta
G: Photosystem II Psb31 protein domain-containing protein
g: Photosystem II Psb31 protein domain-containing protein
H: Photosystem II reaction center protein H
h: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
i: Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
j: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
k: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
l: Photosystem II reaction center protein L
M: Photosystem II reaction center M protein, plastid
m: Photosystem II reaction center M protein, plastid
n: Photosystem II subunit, PsbN.
N: Photosystem II subunit, PsbN.
O: Oxygen-evolving enhancer protein 1
o: Oxygen-evolving enhancer protein 1
T: Photosystem II reaction center protein T
t: Photosystem II reaction center protein T
U: PS II complex 12 kDa extrinsic protein
u: PS II complex 12 kDa extrinsic protein
V: Cytochrome c-550
v: Cytochrome c-550
W: Photosystem II subunit, PsbW
w: Photosystem II subunit, PsbW
X: Photosystem II reaction center X protein
x: Photosystem II reaction center X protein
Z: Photosystem II reaction center protein Z
z: Photosystem II reaction center protein Z
3: Fucoxanthin chl a/c protein, lhca clade
4: Fucoxanthin-chlorophyll a-c binding protein, plastid
5: Fucoxanthin chlorophyll a/c protein 6
6: Fucoxanthin chlorophyll a/c protein 5
7: Fucoxanthin chlorophyll a/c protein-LI818 clade
a: Photosystem II protein D1
b: Photosystem II CP47 reaction center protein
Y: Photosystem II reaction center protein Ycf12
y: Photosystem II reaction center protein Ycf12
Q: Photosystem II subunit, PsbQ.
q: Photosystem II subunit, PsbQ.
0: Fucoxanthin chlorophyll a/c protein-LI818 clade
9: Fucoxanthin chlorophyll a/c light-harvesting protein, major type
2: Fucoxanthin chlorophyll a/c light-harvesting protein, major type
8: Fucoxanthin chlorophyll a/c light-harvesting protein, major type
1: Fucoxanthin chlorophyll a/c light-harvesting protein, major type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,220,690403
Polymers948,01656
Non-polymers272,674347
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem II ... , 18 types, 36 molecules AaBbCcDdGgHhIiJjKkLlMmnNTtWwXx...

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


Mass: 36982.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0W2, photosystem II
#2: Protein Photosystem II CP47 reaction center protein /


Mass: 56465.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0P5
#3: Protein Photosystem II CP43 reaction center protein / / PSII 43 kDa protein / Protein CP-43


Mass: 51776.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0T1
#4: Protein Photosystem II D2 protein / / PSII D2 protein / Photosystem Q(A) protein


Mass: 39089.582 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0T0, photosystem II
#7: Protein Photosystem II Psb31 protein domain-containing protein /


Mass: 18176.705 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8CC14
#8: Protein Photosystem II reaction center protein H / / PSII-H


Mass: 7391.801 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0P8
#9: Protein/peptide Photosystem II reaction center protein I / / PSII-I / PSII 4.8 kDa protein


Mass: 3940.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0U9
#10: Protein/peptide Photosystem II reaction center protein J / / PSII-J


Mass: 4045.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0T9
#11: Protein/peptide Photosystem II reaction center protein K / / PSII-K


Mass: 4983.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0S8
#12: Protein/peptide Photosystem II reaction center protein L / / PSII-L


Mass: 4367.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0U0
#13: Protein Photosystem II reaction center M protein, plastid /


Mass: 12051.050 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8BYH2
#14: Protein/peptide Photosystem II subunit, PsbN. /


Mass: 2571.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Author stated that sequence was not found / Source: (natural) Thalassiosira pseudonana (Diatom)
#16: Protein/peptide Photosystem II reaction center protein T / / PSII-T


Mass: 3314.011 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0P6
#19: Protein Photosystem II subunit, PsbW /


Mass: 6096.549 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8C8Y3
#20: Protein/peptide Photosystem II reaction center X protein /


Mass: 3933.643 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0N4
#21: Protein Photosystem II reaction center protein Z /


Mass: 6417.546 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0T3
#27: Protein/peptide Photosystem II reaction center protein Ycf12 /


Mass: 3591.463 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0T2
#28: Protein Photosystem II subunit, PsbQ. /


Mass: 22439.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8BSY9

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

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


Mass: 9521.692 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0U2
#6: Protein/peptide Cytochrome b559 subunit beta / / PSII reaction center subunit VI


Mass: 4913.846 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0U1

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Protein , 5 types, 8 molecules OoUuVv34

#15: Protein Oxygen-evolving enhancer protein 1


Mass: 32168.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8C4I5
#17: Protein PS II complex 12 kDa extrinsic protein


Mass: 15486.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8BVI4
#18: Protein Cytochrome c-550 / Cytochrome c550


Mass: 17713.232 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: A0T0N2
#22: Protein Fucoxanthin chl a/c protein, lhca clade


Mass: 24100.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8BUU4
#23: Protein Fucoxanthin-chlorophyll a-c binding protein, plastid


Mass: 21058.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8BVI1

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Fucoxanthin chlorophyll a/c ... , 4 types, 8 molecules 56709281

#24: Protein Fucoxanthin chlorophyll a/c protein 6


Mass: 20872.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8BX92
#25: Protein Fucoxanthin chlorophyll a/c protein 5


Mass: 21402.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8CEV5
#26: Protein Fucoxanthin chlorophyll a/c protein-LI818 clade


Mass: 21279.365 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B5YLU3
#29: Protein
Fucoxanthin chlorophyll a/c light-harvesting protein, major type


Mass: 20786.684 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8BX93

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Sugars , 2 types, 17 molecules

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


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C51H96O15
#43: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 17 types, 330 molecules

#30: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56
#31: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5
#32: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#33: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 183 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#34: Chemical
ChemComp-PHO / PHEOPHYTIN A / Pheophytin


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#35: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#36: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#37: 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.: 12 / Source method: obtained synthetically / Formula: C41H78O12S
#39: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C45H86O10
#40: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#41: 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 / Plastoquinone


Mass: 749.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C53H80O2
#42: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#44: Chemical ChemComp-KC1 / Chlorophyll c1 / Chlorophyll c


Mass: 610.941 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H30MgN4O5
#45: Chemical...
ChemComp-A86 / (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate / Fucoxanthin / Fucoxanthin


Mass: 658.906 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C42H58O6
#46: Chemical
ChemComp-DD6 / (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol / Diadinoxanthin / Diadinoxanthin


Mass: 582.855 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C40H54O3
#47: Chemical
ChemComp-KC2 / Chlorophyll c2 / Chlorophyll c


Mass: 608.926 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C35H28MgN4O5
#48: Chemical ChemComp-ET4 / (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol / Diatoxanthin


Mass: 566.856 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H54O2

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Details

Has ligand of interestY

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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

ComponentName: Structure of PSII-FCPII supercomplex containing monomeric LHCX and dimeric FCPII from Thalassiosira pseudonana
Type: COMPLEX / Entity ID: #1-#29 / Source: NATURAL
Source (natural)Organism: Thalassiosira pseudonana (Diatom)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97098 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00578761
ELECTRON MICROSCOPYf_angle_d0.742108968
ELECTRON MICROSCOPYf_dihedral_angle_d16.41226321
ELECTRON MICROSCOPYf_chiral_restr0.04210181
ELECTRON MICROSCOPYf_plane_restr0.00613743

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