Research ArticlePLANT SCIENCES

Structure of cyanobacterial phycobilisome core revealed by structural modeling and chemical cross-linking

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Science Advances  06 Jan 2021:
Vol. 7, no. 2, eaba5743
DOI: 10.1126/sciadv.aba5743
  • Fig. 1 Model construction of a tricylindrical cyanobacterial PBS core.

    (A) Cartoon illustration of disc extension based on PpPBS core structure [Protein Data Bank (PDB) ID: 6KGX] and cyanobacterial structure. PpApcA (salmon), PpApcB (cyan), ApcA (cyanobacteria, purple), and ApcB (dark blue). (B) Detailed representation of disc extension based on PpPBS core structure and cyanobacterial structure. Disc extension of PpPBS core using ApcA/B hexamer, cartoon (A) or x-ray structure (B) (PDB ID: 4F0U). Other Apc domains, i.e., αLCM (green), ApcE-LD1 (green), ApcE-LD2 (green), ApcE-LD3 (green), ApcD (yellow), and ApcF (light cyan), are constructed similarly. The final core model of sPBS is shown (side view). All structure figures in (B) were prepared using PyMOL.

  • Fig. 2 Identified cross-links in different types of sPBS.

    The subunit cross-linking networks, prepared by Cytoscape (41), are shown for (A) WT-sPBS and two mutants including (B) CK-PBS and (C) CpcL-PBS. Cartoon representation of each PBS type is shown in the inset of each panel (top left), where WT-sPBS consists of six rods and a tricylindrical core. CK-PBS contains only a tricylindrical core, and CpcL-PBS is a single rod. The numbers represent the location of the cross-linked residues in each subunit (octagon). ApcA (light pink), ApcB (light purple), ApcC (gray), ApcD (yellow), ApcE (green), and ApcF (cyan). CpcA/B (blue), all other linker proteins (gray)

  • Fig. 3 sPBS core structure evaluated by observed cross-links.

    (A) Side view (cylinder perpendicular to the screen) and (B) side view (cylinder parallel to the screen) and (C) another view of (B) with two bottom cylinders removed, showing first two linker domains of ApcE, i.e., LD1/LD1′ and LD2/LD2′, respectively. (D) ApcE-LD3-K722 is cross-linked to ApcA-K6 and ApcB-NT. (E) ApcC-K52 is surrounded by three ApcB-K113. (F) ApcE-LD1-K331 to ApcA-K6 in basal cylinder. (G) Inter-cylindrical cross-link, ApcA-K27–ApcA-K52. (H) Inter-cylindrical cross-link, ApcB-K17–ApcB-K28. (I to K) Inter-hexameric cross-link, ApcB-K26–ApcB-K53. ApcA (light pink), ApcB (blue), ApcC (orange), ApcD (yellow), ApcE (green), and ApcF (cyan).

  • Fig. 4 The sPBS core structure reveals an acute X-shape of the two basal cylinders.

    (A) Crossover (side view) of the two basal cylinders, front relative to another (back). Dashed-dotted lines show the general trend of the two sets of linker domains, adopting an acute 28° angle relative to each other. ApcE/ApcE′ (green/teal). ApcC (orange). (B) PBS core sitting on the top of PSII (fully stretched), showing two cavities between uneven PBS basal cylinders and PSII (dark green) that allow orange carotenoid proteins (OCPs) (wheat with red pigment) to interact at the putative geometry. (C) Another view of PBS core (fully stretched) sitting on one PSII dimer. It is the tilting of one end of each basal cylinder that allows access of molecules, such as OCP. (D) Amino acid residues (purple sphere) that are involved in cross-linking to PBS core subunits.

  • Fig. 5 PBS bilins and energy transfer pathways.

    (A) Overview of PBS core bilins in a side view (cylinder perpendicular to the screen) sitting on a PSII dimer (green cartoon). αβPCB are colored as purple and blue, respectively. (B) Side view of top cylinder (parallel to the screen). (C and D) Top cylinder showing disc/bilins twisting in a clockwise-counterclockwise-clockwise fashion, cylinder perpendicular to the screen in (D). (E and F) Cylinder disc/bilins twisting in basal cylinder, cylinder perpendicular to the screen in (F). (G) Overview of terminal energy emitter (TEE) excitation energy transfer pathway in PBS-core-PSII complex in a side view. Bilins are labeled. (H) Orientation of inter-cylindrical bilins.

Supplementary Materials

  • Supplementary Materials

    Structure of cyanobacterial phycobilisome core revealed by structural modeling and chemical cross-linking

    Haijun Liu, Mengru M. Zhang, Daniel A. Weisz, Ming Cheng, Himadri B. Pakrasi, Robert E. Blankenship

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