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Structure paper

TitleA structure of the relict phycobilisome from a thylakoid-free cyanobacterium.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 8009, Year 2023
Publish dateDec 4, 2023
AuthorsHan-Wei Jiang / Hsiang-Yi Wu / Chun-Hsiung Wang / Cheng-Han Yang / Jui-Tse Ko / Han-Chen Ho / Ming-Daw Tsai / Donald A Bryant / Fay-Wei Li / Meng-Chiao Ho / Ming-Yang Ho /
PubMed AbstractPhycobilisomes (PBS) are antenna megacomplexes that transfer energy to photosystems II and I in thylakoids. PBS likely evolved from a basic, inefficient form into the predominant hemidiscoidal shape ...Phycobilisomes (PBS) are antenna megacomplexes that transfer energy to photosystems II and I in thylakoids. PBS likely evolved from a basic, inefficient form into the predominant hemidiscoidal shape with radiating peripheral rods. However, it has been challenging to test this hypothesis because ancestral species are generally inaccessible. Here we use spectroscopy and cryo-electron microscopy to reveal a structure of a "paddle-shaped" PBS from a thylakoid-free cyanobacterium that likely retains ancestral traits. This PBS lacks rods and specialized ApcD and ApcF subunits, indicating relict characteristics. Other features include linkers connecting two chains of five phycocyanin hexamers (CpcN) and two core subdomains (ApcH), resulting in a paddle-shaped configuration. Energy transfer calculations demonstrate that chains are less efficient than rods. These features may nevertheless have increased light absorption by elongating PBS before multilayered thylakoids with hemidiscoidal PBS evolved. Our results provide insights into the evolution and diversification of light-harvesting strategies before the origin of thylakoids.
External linksNat Commun / PubMed:38049400 / PubMed Central
MethodsEM (single particle)
Resolution2.38 - 3.97 Å
Structure data

EMDB-35530: Cryo-EM structure of cyanobacterial phycobilisome from Anthocerotibacter panamensis
Method: EM (single particle) / Resolution: 2.99 Å

EMDB-35531: Focused refinement cryo-EM map of A1-A2 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster A-1, Map01)
Method: EM (single particle) / Resolution: 2.64 Å

EMDB-35534: Focused refinement cryo-EM map of A3-A4 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster A-2, Map02)
Method: EM (single particle) / Resolution: 2.64 Å

EMDB-35537: Focused refinement cryo-EM map of B'1-B'2 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster A-3, Map03)
Method: EM (single particle) / Resolution: 2.48 Å

EMDB-35541: Focused refinement cryo-EM map of C'1-C'2 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster A-4, Map04)
Method: EM (single particle) / Resolution: 2.52 Å

EMDB-35542: Focused refinement cryo-EM map of A'1-A'2 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster B-1, Map05)
Method: EM (single particle) / Resolution: 2.73 Å

EMDB-35544: Focused refinement cryo-EM map of A'3-A'4 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster B-2, Map06)
Method: EM (single particle) / Resolution: 2.63 Å

EMDB-35546: Focused refinement cryo-EM map of B1-B2 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster B-3, Map07)
Method: EM (single particle) / Resolution: 2.47 Å

EMDB-35548: Focused refinement cryo-EM map of C1-C2 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster B-4, Map08)
Method: EM (single particle) / Resolution: 2.52 Å

EMDB-35549: Focused refinement cryo-EM map of D3-D4 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster C-1, Map09)
Method: EM (single particle) / Resolution: 2.38 Å

EMDB-35550: Focused refinement cryo-EM map of D1-D2 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster C-2, Map10)
Method: EM (single particle) / Resolution: 2.53 Å

EMDB-35551: Focused refinement cryo-EM map of D'3-D'4 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster C-3, Map11)
Method: EM (single particle) / Resolution: 2.39 Å

EMDB-35552: Focused refinement cryo-EM map of D'1-D'2 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster C-4, Map12)
Method: EM (single particle) / Resolution: 2.54 Å

EMDB-35553: Focused refinement cryo-EM map of Rs2I-Rs2II cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster D-1, Map13)
Method: EM (single particle) / Resolution: 2.79 Å

EMDB-35554: Focused refinement cryo-EM map of Rs1I-Rs1II cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster D-2, Map14)
Method: EM (single particle) / Resolution: 2.74 Å

EMDB-35555: Focused refinement cryo-EM map of RbI-RbII cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster D-3, Map15)
Method: EM (single particle) / Resolution: 3.13 Å

EMDB-35556: Focused refinement cryo-EM map of Rs2'I-Rs2'II cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster E-1, Map16)
Method: EM (single particle) / Resolution: 2.89 Å

EMDB-35557: Focused refinement cryo-EM map of Rs1'I-Rs1'II cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster E-2, Map17)
Method: EM (single particle) / Resolution: 2.86 Å

EMDB-35558: Focused refinement cryo-EM map of Rb'I-Rb'II cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster E-3, Map18)
Method: EM (single particle) / Resolution: 3.05 Å

EMDB-35559: Focused refinement cryo-EM map of Rt1I-Rt1II cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster F-1, Map19)
Method: EM (single particle) / Resolution: 3.23 Å

EMDB-35560: Focused refinement cryo-EM map of Rt2'I-Rt2'II cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster F-2, Map20)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-35561: Focused refinement cryo-EM map of Rt3I-Rt3II cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster F-3, Map21)
Method: EM (single particle) / Resolution: 3.91 Å

EMDB-35562: Focused refinement cryo-EM map of Rt1'I-Rt1'II cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster G-1, Map22)
Method: EM (single particle) / Resolution: 3.22 Å

EMDB-35563: Focused refinement cryo-EM map of Rt2I-Rt2II cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster G-2, Map23)
Method: EM (single particle) / Resolution: 3.29 Å

EMDB-35564: Focused refinement cryo-EM map of Rt3'I-Rt3'II cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster G-3, Map24)
Method: EM (single particle) / Resolution: 3.97 Å

35565

8imi

EMDB-35565: Composite cryo-EM map for A1-A2, A3-A4, B'1-B'2, C'1-C'2 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster A)
PDB-8imi: A1-A2, A3-A4, B'1-B'2, C'1-C'2 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster A)
Method: EM (single particle) / Resolution: 2.59 Å

35566

8imj

EMDB-35566: Composite cryo-EM map for A'1-A'2, A'3-A'4, B1-B2, C1-C2 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster B)
PDB-8imj: A'1-A'2, A'3-A'4, B1-B2, C1-C2 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster B)
Method: EM (single particle) / Resolution: 2.59 Å

35567

8imk

EMDB-35567: Composite cryo-EM map for D3-D4, D1-D2, D'3-D'4, D'1-D'2 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster C)
PDB-8imk: D3-D4, D1-D2, D'3-D'4, D'1-D'2 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster C)
Method: EM (single particle) / Resolution: 2.48 Å

35568

8iml

EMDB-35568: Composite cryo-EM map for Rs2I-Rs2II, Rs1I-Rs1II, RbI-RbII cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster D)
PDB-8iml: Rs2I-Rs2II, Rs1I-Rs1II, RbI-RbII cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster D)
Method: EM (single particle) / Resolution: 2.74 Å

35569

8imm

EMDB-35569: Composite cryo-EM map for Rs2'I-Rs2'II, Rs1'I-Rs1'II, Rb'I-Rb'II cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster E)
PDB-8imm: Rs2'I-Rs2'II, Rs1'I-Rs1'II, Rb'I-Rb'II cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster E)
Method: EM (single particle) / Resolution: 2.76 Å

35570

8imn

EMDB-35570: Composite cryo-EM map for Rt1I-Rt1II, Rt2'I-Rt2'II, Rt3I-Rt3II cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster F)
PDB-8imn: Rt1I-Rt1II, Rt2'I-Rt2'II, Rt3I-Rt3II cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster F)
Method: EM (single particle) / Resolution: 3.07 Å

35571

8imo

EMDB-35571: Composite cryo-EM map for Rt1'I-Rt1'II, Rt2I-Rt2II, Rt3'I-Rt3'II cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster G)
PDB-8imo: Rt1'I-Rt1'II, Rt2I-Rt2II, Rt3'I-Rt3'II cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster G)
Method: EM (single particle) / Resolution: 3.08 Å

Chemicals

ChemComp-CYC:
PHYCOCYANOBILIN

Source
  • anthocerotibacter panamensis (bacteria)
KeywordsPHOTOSYNTHESIS / Complex

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