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Entry
Database: PDB / ID: 8j5k
TitleStructural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana
Components
  • FCPII-G, fucoxanthin chlorophyll a/c binding protein
  • FCPII-H1, fucoxanthin chlorophyll a/c binding protein
  • FCPII-H2, fucoxanthin chlorophyll a/c binding protein
  • FCPII-I, fucoxanthin chlorophyll a/c binding protein
  • FCPII-J, fucoxanthin chlorophyll a/c binding protein
  • FCPII-K, fucoxanthin chlorophyll a/c binding protein
  • Psb34
  • PsbA
  • PsbB
  • PsbC
  • PsbD
  • PsbE
  • PsbF
  • PsbH
  • PsbI
  • PsbJ
  • PsbK
  • PsbL
  • PsbM
  • PsbO
  • PsbQ'
  • PsbT
  • PsbU
  • PsbV
  • PsbW
  • PsbX
  • PsbY
  • PsbZ
KeywordsPHOTOSYNTHESIS / PSII-FCPII supercomplex
Function / homology
Function and homology information


Chem-A86 / BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-ET4 / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE ...Chem-A86 / BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-ET4 / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD
Similarity search - Component
Biological speciesStephanocyclus meneghinianus (Diatom)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsShen, L.L. / Li, Z.H. / Shen, J.R. / Wang, W.D.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2023
Title: Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana.
Authors: Songhao Zhao / Lili Shen / Xiaoyi Li / Qiushuang Tao / Zhenhua Li / Caizhe Xu / Cuicui Zhou / Yanyan Yang / Min Sang / Guangye Han / Long-Jiang Yu / Tingyun Kuang / Jian-Ren Shen / Wenda Wang /
Abstract: Diatoms are dominant marine algae and contribute around a quarter of global primary productivity, the success of which is largely attributed to their photosynthetic capacity aided by specific ...Diatoms are dominant marine algae and contribute around a quarter of global primary productivity, the success of which is largely attributed to their photosynthetic capacity aided by specific fucoxanthin chlorophyll-binding proteins (FCPs) to enhance the blue-green light absorption under water. We purified a photosystem II (PSII)-FCPII supercomplex and a trimeric FCP from Cyclotella meneghiniana (Cm) and solved their structures by cryo-electron microscopy (cryo-EM). The structures reveal detailed organizations of monomeric, dimeric and trimeric FCP antennae, as well as distinct assemblies of Lhcx6_1 and dimeric FCPII-H in PSII core. Each Cm-PSII-FCPII monomer contains an Lhcx6_1, an FCP heterodimer and other three FCP monomers, which form an efficient pigment network for harvesting energy. More diadinoxanthins and diatoxanthins are found in FCPs, which may function to quench excess energy. The trimeric FCP contains more chlorophylls c and fucoxanthins. These diversified FCPs and PSII-FCPII provide a structural basis for efficient light energy harvesting, transfer, and dissipation in C. meneghiniana.
History
DepositionApr 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PsbA
B: PsbB
C: PsbC
D: PsbD
E: PsbE
F: PsbF
H: PsbH
I: PsbI
J: PsbJ
K: PsbK
L: PsbL
M: PsbM
N: Psb34
O: PsbO
Q: PsbQ'
T: PsbT
U: PsbU
V: PsbV
W: PsbW
X: PsbX
Y: PsbY
Z: PsbZ
a: PsbA
b: PsbB
c: PsbC
d: PsbD
e: PsbE
f: PsbF
h: PsbH
i: PsbI
j: PsbJ
k: PsbK
l: PsbL
m: PsbM
n: Psb34
o: PsbO
q: PsbQ'
t: PsbT
u: PsbU
v: PsbV
w: PsbW
x: PsbX
y: PsbY
z: PsbZ
5: FCPII-G, fucoxanthin chlorophyll a/c binding protein
7: FCPII-H2, fucoxanthin chlorophyll a/c binding protein
6: FCPII-H1, fucoxanthin chlorophyll a/c binding protein
p: FCPII-I, fucoxanthin chlorophyll a/c binding protein
4: FCPII-K, fucoxanthin chlorophyll a/c binding protein
3: FCPII-J, fucoxanthin chlorophyll a/c binding protein
P: FCPII-I, fucoxanthin chlorophyll a/c binding protein
9: FCPII-K, fucoxanthin chlorophyll a/c binding protein
8: FCPII-J, fucoxanthin chlorophyll a/c binding protein
0: FCPII-G, fucoxanthin chlorophyll a/c binding protein
2: FCPII-H2, fucoxanthin chlorophyll a/c binding protein
1: FCPII-H1, fucoxanthin chlorophyll a/c binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,107,524392
Polymers837,46056
Non-polymers270,064336
Water0
1


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

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Components

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Protein , 17 types, 34 molecules AaBbCcDdEeHhOoQqUuVvZz507261pP...

#1: Protein PsbA


Mass: 36951.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#2: Protein PsbB


Mass: 53504.957 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#3: Protein PsbC


Mass: 49357.348 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#4: Protein PsbD


Mass: 37826.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#5: Protein PsbE


Mass: 8687.784 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#7: Protein PsbH


Mass: 7188.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#14: Protein PsbO


Mass: 26749.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#15: Protein PsbQ'


Mass: 16001.864 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#17: Protein PsbU


Mass: 10010.334 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#18: Protein PsbV


Mass: 14757.663 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#22: Protein PsbZ


Mass: 6233.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#23: Protein FCPII-G, fucoxanthin chlorophyll a/c binding protein


Mass: 18512.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#24: Protein FCPII-H2, fucoxanthin chlorophyll a/c binding protein


Mass: 18251.734 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#25: Protein FCPII-H1, fucoxanthin chlorophyll a/c binding protein


Mass: 18085.545 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#26: Protein FCPII-I, fucoxanthin chlorophyll a/c binding protein


Mass: 23279.170 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#27: Protein FCPII-K, fucoxanthin chlorophyll a/c binding protein


Mass: 13039.064 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#28: Protein FCPII-J, fucoxanthin chlorophyll a/c binding protein


Mass: 17850.197 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)

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Protein/peptide , 11 types, 22 molecules FfIiJjKkLlMmNnTtWwXxYy

#6: Protein/peptide PsbF


Mass: 3555.263 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#8: Protein/peptide PsbI


Mass: 3940.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#9: Protein/peptide PsbJ


Mass: 3487.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#10: Protein/peptide PsbK


Mass: 4225.085 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#11: Protein/peptide PsbL


Mass: 4235.880 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#12: Protein/peptide PsbM


Mass: 4358.022 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#13: Protein/peptide Psb34


Mass: 2571.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#16: Protein/peptide PsbT


Mass: 3441.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#19: Protein/peptide PsbW


Mass: 5606.405 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#20: Protein/peptide PsbX


Mass: 3389.061 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#21: Protein/peptide PsbY


Mass: 3634.343 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)

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Sugars , 1 types, 8 molecules

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


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 15 types, 328 molecules

#29: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical ChemComp-FE2 / FE (II) ION


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


Mass: 893.489 Da / Num. of mol.: 206 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical
ChemComp-PHO / PHEOPHYTIN A / Pheophytin


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5 / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56
#34: 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.: 8 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#35: 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.: 4 / Source method: obtained synthetically / Formula: C53H80O2 / Feature type: SUBJECT OF INVESTIGATION
#36: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#37: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#38: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#40: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#41: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#42: 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.: 24 / Source method: obtained synthetically / Formula: C42H58O6 / Feature type: SUBJECT OF INVESTIGATION
#43: 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 / Feature type: SUBJECT OF INVESTIGATION
#44: 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.: 12 / Source method: obtained synthetically / Formula: C40H54O3 / Feature type: SUBJECT OF INVESTIGATION

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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: Cm-PSII-FCPII / Type: COMPLEX / Entity ID: #1-#28 / Source: NATURAL
Source (natural)Organism: Stephanocyclus meneghinianus (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: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 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: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153326 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00475624
ELECTRON MICROSCOPYf_angle_d0.933106276
ELECTRON MICROSCOPYf_dihedral_angle_d15.66412881
ELECTRON MICROSCOPYf_chiral_restr0.04710228
ELECTRON MICROSCOPYf_plane_restr0.00713531

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