In situ cryo-ET structure of phycobilisome–photosystem II supercomplex from red alga
- Key Laboratory for Protein Sciences of Ministry of Education, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, China
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, China
- Department of Biology, Southern University of Science and Technology, China
Figures
Figure 1 with 1 supplement
Organization of PBS–PSII supercomplexes on the thylakoid membrane.
(A) Representative tomogram slice in cross-section view. The box represents magnified details of PBS, a PSII dimer, the thylakoid membrane, and the lumen. (B) Spatial mapping of the PBS–PSII …
Figure 1—figure supplement 1
Tomographic slice of the whole cell and the PBS–PSII supercomplexes on the thylakoid membrane.
(A) Representative cross-section view of the whole cell. The PBS–PSII supercomplexes are neatly packed in most regions, while some PBS–PSII supercomplexes are randomly distributed. (B) …
Figure 2 with 5 supplements
Overview of the PBS–PSII and double PBS–PSII structures.
(A) The density map of double PBS–PSII structures at a resolution of 15.6 Å, presented in two perpendicular views. The center-to-center distance of two adjacent PBSs is approximately 345 Å. Two …
Figure 2—figure supplement 1
Resolution estimation and the ResMap analysis of the density maps for the double PBS–PSII supercomplex and the PBS–PSII supercomplex.
(A) The ‘gold-standard’ Fourier shell correlation (FSC) curves calculated between two halves of datasets for the double PBS–PSII supercomplex (15.6 Å), the PBS–PSII supercomplex (14.3 Å), and the …
Figure 2—figure supplement 2
Sub-tomogram structural analysis of the PBS–PSII supercomplex.
(A, B) Conformational change of β-subunit interspersed between Rod e and Rod d'. β-subunitSPA in green is the model built with the map of single particle analysis, and β-subunitCryoET in red is the …
Figure 2—figure supplement 3
Sub-tomogram map analysis of the double PBS–PSII supercomplex, the PBS–PSII supercomplex, and the PBS–PSII supercomplex with post-processing.
(A) Overall structure of the double PBS–PSII supercomplex (surface threshold, 0.09). (B) Slice view shows the row of PSII dimers indicated in (A). (C) The overall structure of the PBS–PSII …
Figure 2—figure supplement 4
PSII sequence analysis of Porphyridium purpureum and Cyanidium caldarium.
(A) Sequence homogeneity alignment of each subunit of PSII between P. purpureum (Pp) and C. caldarium (Cc) indicates that most of the subunits are highly conserved. (B) Maximum likelihood (ML) …
Figure 2—figure supplement 5
Geometry of PBS and PSIIs.
(A) The bottom view of the PBS–PSII supercomplex fitting model shows that the face plane of the PSII dimers A and B rotates approximately 14° along the PBS core plane. The centers of the two PSII …
Figure 3 with 1 supplement
The connections between PBS and PSIIs.
(A, B) A segmentation map of two basal cylinders of the PBS core (labeled as a and a', respectively) and PSII dimers A and B (each monomer is labeled as A1, A2, B1, and B2, respectively). Each basal …
Figure 3—figure supplement 1
Map extraction model of the PBS–PSII supercomplex.
To analyze the connections between PBS and PSII, we extracted the part two densities from the PBS–PSII supercomplex, include PBS core cylinders a, a', PSII dimers A and B. The extraction was …
Figure 4 with 2 supplements
Three connector proteins in the PBS–PSII supercomplex.
(A) Overall structure of the PBS–PSII supercomplex (surface threshold of 0.065), highlighting the PBS core, Rod a of PBS, connector 1, and connector 2 between PBS and PSII. (B, C) The magnified clip …
Figure 4—figure supplement 1
Extra density analysis of the PBS–PSII supercomplex and the double PBS–PSII supercomplex.
(A) To analyze the density map, we carefully docked the cryo-EM model of PBS, X-ray model of PSII dimer, and two lateral hexamers into the PBS–PSII supercomplex map. Two extra solid densities cannot …
Figure 4—figure supplement 2
Structures of connectors 1, 2, and 3.
To measure the geometry of the three connectors’ density map, we segmented the densities of connectors 1 and 2 from the PBS–PSII supercomplex with post-processing and that of connector 3 from the …
Figure 5
Schematic model of the PBS–PSII supercomplex.
(A) The front view of the schematic model of the PBS–PSII supercomplex. For PBS, only core and Rod a are represented for clarity. In the PBS core, a and a' represent the two basal cylinders. Each …
Figure 6
The thylakoid membrane builds perforations and stairs by branching and fusing with the neighboring membrane.
(A) Typical tomogram slice. The white box indicates the tomogram region shown in Figure 1A; red box represents the membrane branching and fusing area. Scale bar, 100 nm. (B) Sequential slices back …
Videos
Video 1
Sequential slices back and forth through the representative tomogram in cross-section view.
Related to Figure 1. Scale bar, 100 nm.
Video 2
Sequential slices back and forth through the representative tomogram slice in cross-section view.
Related to Figure 1—figure supplement 1B. The color boxes indicate the two types of the tight perforations. Scale bar, 100 nm.
Video 3
Sequential slices back and forth through the representative tomogram slice in cross-section view.
Related to Figure 1—figure supplement 1C. Scale bar, 100 nm.
Video 4
Clip views of the segmentation map of two basal cylinders of the PBS.
Related to Figure 3.
Video 5
Sequential slices back and forth through the representative tomogram slice to show thylakoid membrane branching and fusing areas.
Related to Figure 6A–E. Scale bar, 20 nm.
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Porphyridium purpureum) | Porphyridium purpureum UTEX 2757 | https://utex.org/products/utex-lb-2757 | UTEX Culture Collection of Algae 2,757 | |
| Gene (Porphyridium purpureum) | uniprot | https://www.uniprot.org/uniprot/ | UP000324585 | Proteome |
| Software, algorithm | SerialEM | https://bio3d.colorado.edu/SerialEM/ | Version 3.1.8 | Data collection |
| Software, algorithm | Chimera | https://www.cgl.ucsf.edu/chimera/ | Version 10.15 | Visualization |
| Software, algorithm | Relion | https://www3.mrc-lmb.cam.ac.uk/relion/ | Version 2.1 | Subtomogram averaging |
| Software, algorithm | IMOD | https://bio3d.colorado.edu/imod/index.html | Version 4.9 | Tomogram reconstruction |
| Software, algorithm | TOMO3D | https://sites.google.com/site/3dem/imageprocessing/tomo3d | Version 2.0 | Tomogram reconstruction |
| Software, algorithm | I3 | https://www.electrontomography.org/ | Version 0.9.3 | Subtomogram averaging |
Additional files
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Supplementary file 1
Cross-correlation coefficient (CCC) of crystal structures or single particle analysis model and sub-tomogram averaging map.
- https://cdn.elifesciences.org/articles/69635/elife-69635-supp1-v1.docx
-
Transparent reporting form
- https://cdn.elifesciences.org/articles/69635/elife-69635-transrepform1-v1.docx
