4XXI

Crystal structure of the Bilin-binding domain of phycobilisome core-membrane linker ApcE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The terminal phycobilisome emitter, LCM: A light-harvesting pigment with a phytochrome chromophore

Tang, K.Ding, W.-L.Hoppner, A.Zhao, C.Zhang, L.Hontani, Y.Kennis, J.T.M.Gartner, W.Scheer, H.Zhou, M.Zhao, K.-H.

(2015) Proc Natl Acad Sci U S A 112: 15880-15885

  • DOI: https://doi.org/10.1073/pnas.1519177113
  • Primary Citation of Related Structures:  
    4XXI, 4XXK

  • PubMed Abstract: 

    Photosynthesis relies on energy transfer from light-harvesting complexes to reaction centers. Phycobilisomes, the light-harvesting antennas in cyanobacteria and red algae, attach to the membrane via the multidomain core-membrane linker, L(CM). The chromophore domain of L(CM) forms a bottleneck for funneling the harvested energy either productively to reaction centers or, in case of light overload, to quenchers like orange carotenoid protein (OCP) that prevent photodamage. The crystal structure of the solubly modified chromophore domain from Nostoc sp. PCC7120 was resolved at 2.2 Å. Although its protein fold is similar to the protein folds of phycobiliproteins, the phycocyanobilin (PCB) chromophore adopts ZZZssa geometry, which is unknown among phycobiliproteins but characteristic for sensory photoreceptors (phytochromes and cyanobacteriochromes). However, chromophore photoisomerization is inhibited in L(CM) by tight packing. The ZZZssa geometry of the chromophore and π-π stacking with a neighboring Trp account for the functionally relevant extreme spectral red shift of L(CM). Exciton coupling is excluded by the large distance between two PCBs in a homodimer and by preservation of the spectral features in monomers. The structure also indicates a distinct flexibility that could be involved in quenching. The conclusions from the crystal structure are supported by femtosecond transient absorption spectra in solution.


  • Organizational Affiliation

    State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China; Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany;


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobiliprotein ApcE
A, B
157Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: apcEalr0020
UniProt
Find proteins for P80559 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore P80559 
Go to UniProtKB:  P80559
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80559
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.356α = 90
b = 80.552β = 90
c = 115.449γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata processing
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-01-13
    Changes: Database references, Structure summary
  • Version 1.2: 2018-05-16
    Changes: Data collection, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description