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- PDB-7y1a: Lateral hexamer -

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Basic information

Entry
Database: PDB / ID: 7y1a
TitleLateral hexamer
Components
  • (LRH) x 2
  • B-phycoerythrin beta chain
  • Phycoerythrin alpha subunit
KeywordsPHOTOSYNTHESIS / Lateral hexamer / PBS
Function / homology
Function and homology information


phycobilisome / chloroplast thylakoid membrane / photosynthesis
Similarity search - Function
Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
PHYCOERYTHROBILIN / Phycoerythrin alpha subunit / B-phycoerythrin beta chain
Similarity search - Component
Biological speciesPorphyridium purpureum (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsYou, X. / Zhang, X. / Cheng, J. / Xiao, Y.N. / Sun, S. / Sui, S.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2023
Title: In situ structure of the red algal phycobilisome-PSII-PSI-LHC megacomplex.
Authors: Xin You / Xing Zhang / Jing Cheng / Yanan Xiao / Jianfei Ma / Shan Sun / Xinzheng Zhang / Hong-Wei Wang / Sen-Fang Sui /
Abstract: In oxygenic photosynthetic organisms, light energy is captured by antenna systems and transferred to photosystem II (PSII) and photosystem I (PSI) to drive photosynthesis. The antenna systems of red ...In oxygenic photosynthetic organisms, light energy is captured by antenna systems and transferred to photosystem II (PSII) and photosystem I (PSI) to drive photosynthesis. The antenna systems of red algae consist of soluble phycobilisomes (PBSs) and transmembrane light-harvesting complexes (LHCs). Excitation energy transfer pathways from PBS to photosystems remain unclear owing to the lack of structural information. Here we present in situ structures of PBS-PSII-PSI-LHC megacomplexes from the red alga Porphyridium purpureum at near-atomic resolution using cryogenic electron tomography and in situ single-particle analysis, providing interaction details between PBS, PSII and PSI. The structures reveal several unidentified and incomplete proteins and their roles in the assembly of the megacomplex, as well as a huge and sophisticated pigment network. This work provides a solid structural basis for unravelling the mechanisms of PBS-PSII-PSI-LHC megacomplex assembly, efficient energy transfer from PBS to the two photosystems, and regulation of energy distribution between PSII and PSI.
History
DepositionJun 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
y: B-phycoerythrin beta chain
z: Phycoerythrin alpha subunit
1: B-phycoerythrin beta chain
p: Phycoerythrin alpha subunit
q: B-phycoerythrin beta chain
r: Phycoerythrin alpha subunit
s: B-phycoerythrin beta chain
t: Phycoerythrin alpha subunit
u: B-phycoerythrin beta chain
v: Phycoerythrin alpha subunit
w: B-phycoerythrin beta chain
x: Phycoerythrin alpha subunit
a: LRH
A: LRH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,90545
Polymers238,65514
Non-polymers18,25031
Water00
1


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

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Components

#1: Protein
B-phycoerythrin beta chain


Mass: 18584.182 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: cpeB / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: P11393
#2: Protein
Phycoerythrin alpha subunit / R-phycoerythrin alpha subunit


Mass: 17824.029 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: peA, cpeA / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: E2IH77
#3: Protein LRH


Mass: 7422.140 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Production host: Porphyridium purpureum (eukaryote)
#4: Protein LRH


Mass: 12783.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Production host: Porphyridium purpureum (eukaryote)
#5: Chemical...
ChemComp-PEB / PHYCOERYTHROBILIN


Mass: 588.694 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Lateral hexamer of PBS / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Buffer solutionpH: 7
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 6000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87000 / Symmetry type: POINT

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