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- PDB-8w4o: Structure of PSII-FCPII-G/H complex in the PSII-FCPII supercomple... -

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Basic information

Entry
Database: PDB / ID: 8w4o
TitleStructure of PSII-FCPII-G/H complex in the PSII-FCPII supercomplex from 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
KeywordsPHOTOSYNTHESIS / PSII-FCPII
Function / homologyChem-A86 / CHLOROPHYLL A / Chem-DD6 / Chem-ET4 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-SQD
Function and homology information
Biological speciesStephanocyclus meneghinianus (Diatom)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.23 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
DepositionAug 24, 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

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Assembly

Deposited unit
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,61855
Polymers54,8493
Non-polymers42,76952
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 3 molecules 576

#1: Protein FCPII-G, Fucoxanthin chlorophyll a/c binding protein


Mass: 18512.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#2: Protein FCPII-H2, Fucoxanthin chlorophyll a/c binding protein


Mass: 18251.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)
#3: Protein FCPII-H1, Fucoxanthin chlorophyll a/c binding protein


Mass: 18085.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Stephanocyclus meneghinianus (Diatom)

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Non-polymers , 7 types, 52 molecules

#4: 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


Mass: 658.906 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C42H58O6 / Feature type: SUBJECT OF INVESTIGATION
#5: 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.: 1 / Source method: obtained synthetically / Formula: C40H54O2
#6: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#8: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#9: 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.: 1 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#10: 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


Mass: 582.855 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H54O3

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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-G/H / Type: COMPLEX
Details: PSII-FCPII-G/H complex in the PSII-FCPII supercomplex from Cyclotella meneghiniana
Entity ID: #1-#3 / 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 FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 314409 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0056454
ELECTRON MICROSCOPYf_angle_d1.3679432
ELECTRON MICROSCOPYf_dihedral_angle_d20.3891096
ELECTRON MICROSCOPYf_chiral_restr0.055777
ELECTRON MICROSCOPYf_plane_restr0.0091275

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