4XXK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.182 

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Ligand Structure Quality Assessment 


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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: 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 ...

    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; khzhao@163.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phycobiliprotein ApcEA, B157Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: apcEalr0020
EC: 4
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYC
Query on CYC

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.98α = 90
b = 66.59β = 91.07
c = 81.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata processing
XSCALEdata scaling

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