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- EMDB-33558: Lateral hexamer -

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Basic information

Entry
Database: EMDB / ID: EMD-33558
TitleLateral hexamer
Map data
Sample
  • Complex: Lateral hexamer of PBS
    • Protein or peptide: B-phycoerythrin beta chain
    • Protein or peptide: Phycoerythrin alpha subunit
    • Protein or peptide: LRH
    • Protein or peptide: LRH
  • Ligand: PHYCOERYTHROBILIN
Function / homologyPhycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / phycobilisome / chloroplast thylakoid membrane / photosynthesis / Globin-like superfamily / Phycoerythrin alpha subunit / B-phycoerythrin beta chain
Function and homology information
Biological speciesPorphyridium purpureum (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsYou X / Zhang X / Cheng J / Xiao YN / Sun S / Sui SF
Funding support1 items
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, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateApr 19, 2023-
Current statusApr 19, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33558.png

Downloads & links

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Map

FileDownload / File: emd_33558.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 256 pix.
= 417.792 Å		1.63 Å/pix.
x 256 pix.
= 417.792 Å		1.63 Å/pix.
x 256 pix.
= 417.792 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.632 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.152
Minimum - Maximum-2.1009831 - 1.9596292
Average (Standard dev.)-0.0003946878 (±0.051328033)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 417.792 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33558_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33558_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Lateral hexamer of PBS

EntireName: Lateral hexamer of PBS
Components
  • Complex: Lateral hexamer of PBS
    • Protein or peptide: B-phycoerythrin beta chain
    • Protein or peptide: Phycoerythrin alpha subunit
    • Protein or peptide: LRH
    • Protein or peptide: LRH
  • Ligand: PHYCOERYTHROBILIN

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Supramolecule #1: Lateral hexamer of PBS

SupramoleculeName: Lateral hexamer of PBS / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Porphyridium purpureum (eukaryote)

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Macromolecule #1: B-phycoerythrin beta chain

MacromoleculeName: B-phycoerythrin beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 18.584182 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MLDAFSRVVV NSDAKAAYVG GSDLQALKSF IADGNKRLDA VNSIVSNASC MVSDAVSGMI CENPGLISPG G(MEN)CYTN RRM AACLRDGEII LRYVSYALLA GDASVLEDRC LNGLKETYIA LGVPTNSSIR AVSIMKAQAV AFITNTATER KMSFAAG DC TSLASEVASY FDRVGAAIS

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Macromolecule #2: Phycoerythrin alpha subunit

MacromoleculeName: Phycoerythrin alpha subunit / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 17.824029 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MKSVITTVVS AADAAGRFPS NSDLESIQGN IQRSAARLEA AEKLAGNHEA VVKEAGDACF AKYAYLKNPG EAGENQEKIN KCYRDVDHY MRLVNYCLVV GGTGPLDEWG IAGAREVYRT LNLPTSAYVA SIAYTRDRLC VPRDMSAQAG VEFSAYLDYL I NALS

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Macromolecule #3: LRH

MacromoleculeName: LRH / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 7.42214 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #4: LRH

MacromoleculeName: LRH / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 12.78375 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #5: PHYCOERYTHROBILIN

MacromoleculeName: PHYCOERYTHROBILIN / type: ligand / ID: 5 / Number of copies: 31 / Formula: PEB
Molecular weightTheoretical: 588.694 Da
Chemical component information

ChemComp-PEB:
PHYCOERYTHROBILIN

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6kgx

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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