3NPH

Crystal structure of the pfam00427 domain from Synechocystis sp. PCC 6803


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the N-terminal domain of linker L(R) and the assembly of cyanobacterial phycobilisome rods

Gao, X.Zhang, N.Wei, T.-D.Su, H.-N.Xie, B.-B.Dong, C.-C.Zhang, X.-Y.Chen, X.-L.Zhou, B.-C.Wang, Z.-X.Wu, J.-W.Zhang, Y.-Z.

(2011) Mol Microbiol 82: 698-705

  • DOI: 10.1111/j.1365-2958.2011.07844.x
  • Primary Citation of Related Structures:  
    3NPH

  • PubMed Abstract: 
  • Phycobilisomes are light-harvesting supramolecular complexes in cyanobacteria and red algae. Linkers play a pivotal role in the assembly and energy transfer modulation of phycobilisomes. However, how linkers function remains unclear due to the lack o ...

    Phycobilisomes are light-harvesting supramolecular complexes in cyanobacteria and red algae. Linkers play a pivotal role in the assembly and energy transfer modulation of phycobilisomes. However, how linkers function remains unclear due to the lack of structural and biochemical studies of linkers, especially the N-terminal domain of L(R) (pfam00427). Here, we report the crystal structure of the pfam00427 domain of the linker L(R) (30) from Synechocystis sp. PCC 6803 at 1.9 Å. The pfam00427 presents as a previously uncharacterized point symmetric six α-helix bundle. To elucidate the binding style of pfam00427 in the C-phycocyanin (C-PC) (αβ)(6) hexamer, we fixed pfam00427 computationally into the C-PC (αβ)(6) inner cavity using the program AutoDock. Combined with a conserved 'C-PC binding patch' on pfam00427 identified, we arrived at a model for the pfam00427-C-PC (αβ)(6) complex. This model was further optimized and evaluated as a reasonable result by a molecular dynamics simulation. In the resulting model, the pfam00427 domain is stably positioned in the central hole of the C-PC trimer. Moreover, the L(RT) (pfam01383) was docked into our pfam00427-C-PC model to generate a complete phycobilisome rod in which the linkers join individual biliprotein hexamers.


    Organizational Affiliation

    State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2B148Synechocystis sp. PCC 6803Mutation(s): 0 
Find proteins for P73204 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore P73204 
Go to UniProtKB:  P73204
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.675α = 90
b = 55.675β = 90
c = 79.187γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-10-19
    Changes: Database references
  • Version 1.3: 2011-12-14
    Changes: Database references