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- PDB-8j0d: FCP heterodimer, Lhca2, and Lhcf5 together as the M1 side binds t... -

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Basic information

Entry
Database: PDB / ID: 8j0d
TitleFCP heterodimer, Lhca2, and Lhcf5 together as the M1 side binds to the PSII core in the diatom Thalassiosira pseudonana
Components
  • (Fucoxanthin chlorophyll a/c protein ...) x 2
  • Fucoxanthin chl a/c protein, lhca clade
  • Fucoxanthin-chlorophyll a-c binding protein, plastid
KeywordsPHOTOSYNTHESIS / FCP / heterodimer
Function / homology
Function and homology information


light-harvesting complex / photosynthesis, light harvesting in photosystem I / chlorophyll binding / response to light stimulus / chloroplast / membrane
Similarity search - Function
Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein
Similarity search - Domain/homology
Chem-A86 / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c1 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Fucoxanthin chl a/c protein, lhca clade / Fucoxanthin-chlorophyll a-c binding protein, plastid ...Chem-A86 / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c1 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Fucoxanthin chl a/c protein, lhca clade / Fucoxanthin-chlorophyll a-c binding protein, plastid / Fucoxanthin chlorophyll a/c protein 6 / Fucoxanthin chlorophyll a/c protein 5
Similarity search - Component
Biological speciesThalassiosira pseudonana (Diatom)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsLi, Z. / Feng, Y. / Wang, W. / Shen, J.R.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences2021YFA1300403 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
DepositionApr 10, 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,93978
Polymers77,8424
Non-polymers58,09774
Water00
1


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

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Components

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Protein , 2 types, 2 molecules 34

#1: 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
#2: Protein Fucoxanthin-chlorophyll a-c binding protein, plastid


Mass: 17745.100 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 protein ... , 2 types, 2 molecules 56

#3: Protein Fucoxanthin chlorophyll a/c protein 6


Mass: 17614.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8BX92
#4: Protein Fucoxanthin chlorophyll a/c protein 5


Mass: 18380.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thalassiosira pseudonana (Diatom) / References: UniProt: B8CEV5

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Sugars , 2 types, 3 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION
#13: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 7 types, 71 molecules

#5: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-KC1 / Chlorophyll c1


Mass: 610.941 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H30MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#7: 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.: 17 / Source method: obtained synthetically / Formula: C42H58O6 / Feature type: SUBJECT OF INVESTIGATION
#8: 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.: 2 / Source method: obtained synthetically / Formula: C40H54O3 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#12: Chemical ChemComp-KC2 / Chlorophyll c2


Mass: 608.926 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H28MgN4O5 / 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: M1 local refinement in the PSII-FCPII from the Thalassiosira pseudonana at 3.19 angstrom
Type: COMPLEX / Entity ID: #1-#4 / 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 FIELD / 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: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97098 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0069641
ELECTRON MICROSCOPYf_angle_d0.97113369
ELECTRON MICROSCOPYf_dihedral_angle_d15.822924
ELECTRON MICROSCOPYf_chiral_restr0.041013
ELECTRON MICROSCOPYf_plane_restr0.0051798

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