8DDY

Helical rods of far-red light-absorbing allophycocyanin in Synechococcus sp.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Helical allophycocyanin nanotubes absorb far-red light in a thermophilic cyanobacterium.

Gisriel, C.J.Elias, E.Shen, G.Soulier, N.T.Flesher, D.A.Gunner, M.R.Brudvig, G.W.Croce, R.Bryant, D.A.

(2023) Sci Adv 9: eadg0251-eadg0251

  • DOI: https://doi.org/10.1126/sciadv.adg0251
  • Primary Citation of Related Structures:  
    8DDY

  • PubMed Abstract: 

    To compete in certain low-light environments, some cyanobacteria express a paralog of the light-harvesting phycobiliprotein, allophycocyanin (AP), that strongly absorbs far-red light (FRL). Using cryo-electron microscopy and time-resolved absorption spectroscopy, we reveal the structure-function relationship of this FRL-absorbing AP complex (FRL-AP) that is expressed during acclimation to low light and that likely associates with chlorophyll a-containing photosystem I. FRL-AP assembles as helical nanotubes rather than typical toroids due to alterations of the domain geometry within each subunit. Spectroscopic characterization suggests that FRL-AP nanotubes are somewhat inefficient antenna; however, the enhanced ability to harvest FRL when visible light is severely attenuated represents a beneficial trade-off. The results expand the known diversity of light-harvesting proteins in nature and exemplify how biological plasticity is achieved by balancing resource accessibility with efficiency.


  • Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, CT 06520, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin subunit alpha
A, C, E
184Synechococcus sp. 63AY4M1Mutation(s): 0 
Gene Names: SYN60AY4M2_00015
UniProt
Find proteins for A0A2G8PAX6 (Synechococcus sp. 60AY4M2)
Explore A0A2G8PAX6 
Go to UniProtKB:  A0A2G8PAX6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2G8PAX6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin subunit beta
B, D, F
161Synechococcus sp. 63AY4M1Mutation(s): 0 
Gene Names: SYN60AY4M2_00020
UniProt
Find proteins for A0A2G8PA94 (Synechococcus sp. 60AY4M2)
Explore A0A2G8PA94 
Go to UniProtKB:  A0A2G8PA94
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2G8PA94
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYC (Subject of Investigation/LOI)
Query on CYC

Download Ideal Coordinates CCD File 
G [auth A]
H [auth B]
J [auth C]
K [auth D]
M [auth E]
G [auth A],
H [auth B],
J [auth C],
K [auth D],
M [auth E],
N [auth F]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth B],
L [auth D],
O [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
B, D, F
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-1613022
Department of Energy (DOE, United States)United StatesDE-FG02-05ER15646
Department of Energy (DOE, United States)United StatesDE-SC0001423
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesK99GM140174
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM008283

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release