8IML

Rs2I-Rs2II, Rs1I-Rs1II, RbI-RbII cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster D)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A structure of the relict phycobilisome from a thylakoid-free cyanobacterium.

Jiang, H.W.Wu, H.Y.Wang, C.H.Yang, C.H.Ko, J.T.Ho, H.C.Tsai, M.D.Bryant, D.A.Li, F.W.Ho, M.C.Ho, M.Y.

(2023) Nat Commun 14: 8009-8009

  • DOI: https://doi.org/10.1038/s41467-023-43646-9
  • Primary Citation of Related Structures:  
    8IMI, 8IMJ, 8IMK, 8IML, 8IMM, 8IMN, 8IMO

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Department of Life Science, National Taiwan University, Taipei, Taiwan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CpcJA [auth 3]531Anthocerotibacter panamensisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CpcA163Anthocerotibacter panamensisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CpcB172Anthocerotibacter panamensisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CpcDAA [auth Z],
N [auth M],
OA [auth m]
78Anthocerotibacter panamensisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CpcGBA [auth 4]252Anthocerotibacter panamensisMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYC (Subject of Investigation/LOI)
Query on CYC

Download Ideal Coordinates CCD File 
AB [auth H]
AC [auth a]
BB [auth I]
BC [auth b]
CB [auth I]
AB [auth H],
AC [auth a],
BB [auth I],
BC [auth b],
CB [auth I],
CC [auth c],
DB [auth J],
DC [auth d],
EB [auth K],
EC [auth e],
FB [auth K],
FC [auth f],
GB [auth L],
GC [auth g],
HB [auth N],
HC [auth g],
IB [auth O],
IC [auth h],
JB [auth P],
JC [auth h],
KB [auth Q],
KC [auth i],
LB [auth R],
LC [auth j],
MB [auth S],
MC [auth j],
NB [auth T],
NC [auth k],
OB [auth T],
OC [auth k],
PA [auth 3],
PB [auth U],
PC [auth l],
QA [auth A],
QB [auth V],
QC [auth l],
RA [auth A],
RB [auth V],
SA [auth B],
SB [auth W],
TA [auth B],
TB [auth W],
UA [auth C],
UB [auth X],
VA [auth D],
VB [auth X],
WA [auth E],
WB [auth Y],
XA [auth F],
XB [auth Y],
YA [auth G],
YB [auth Z],
ZA [auth G],
ZB [auth 4]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)Taiwan--
National Science Council (NSC, Taiwan)Taiwan--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references