4LM6

Light harvesting complex PC612 from the cryptophyte Hemiselmis virescens M1635


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins.

Harrop, S.J.Wilk, K.E.Dinshaw, R.Collini, E.Mirkovic, T.Teng, C.Y.Oblinsky, D.G.Green, B.R.Hoef-Emden, K.Hiller, R.G.Scholes, G.D.Curmi, P.M.

(2014) Proc Natl Acad Sci U S A 111: E2666-E2675

  • DOI: 10.1073/pnas.1402538111
  • Primary Citation of Related Structures:  
    4LM6, 4LMS, 4LMX

  • PubMed Abstract: 
  • Observation of coherent oscillations in the 2D electronic spectra (2D ES) of photosynthetic proteins has led researchers to ask whether nontrivial quantum phenomena are biologically significant. Coherent oscillations have been reported for the soluble light-harvesting phycobiliprotein (PBP) antenna isolated from cryptophyte algae ...

    Observation of coherent oscillations in the 2D electronic spectra (2D ES) of photosynthetic proteins has led researchers to ask whether nontrivial quantum phenomena are biologically significant. Coherent oscillations have been reported for the soluble light-harvesting phycobiliprotein (PBP) antenna isolated from cryptophyte algae. To probe the link between spectral properties and protein structure, we determined crystal structures of three PBP light-harvesting complexes isolated from different species. Each PBP is a dimer of αβ subunits in which the structure of the αβ monomer is conserved. However, we discovered two dramatically distinct quaternary conformations, one of which is specific to the genus Hemiselmis. Because of steric effects emerging from the insertion of a single amino acid, the two αβ monomers are rotated by ∼73° to an "open" configuration in contrast to the "closed" configuration of other cryptophyte PBPs. This structural change is significant for the light-harvesting function because it disrupts the strong excitonic coupling between two central chromophores in the closed form. The 2D ES show marked cross-peak oscillations assigned to electronic and vibrational coherences in the closed-form PC645. However, such features appear to be reduced, or perhaps absent, in the open structures. Thus cryptophytes have evolved a structural switch controlled by an amino acid insertion to modulate excitonic interactions and therefore the mechanisms used for light harvesting.


    Organizational Affiliation

    School of Physics, The University of New South Wales, Sydney, NSW 2052, Australia;Centre for Applied Medical Research, St Vincent's Hospital, Sydney, NSW 2010, Australia p.curmi@unsw.edu.au.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cryptophyte phycocyanin alpha chainA, C62Hemiselmis virescensMutation(s): 0 
Gene Names: cpeA1
UniProt
Find proteins for C0HM11 (Hemiselmis virescens)
Explore C0HM11 
Go to UniProtKB:  C0HM11
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC0HM11
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cryptophyte phycocyanin beta chainB, D177Hemiselmis virescensMutation(s): 0 
Gene Names: cpeB
UniProt
Find proteins for A0A075B5G2 (Hemiselmis virescens)
Explore A0A075B5G2 
Go to UniProtKB:  A0A075B5G2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A075B5G2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYC
Query on CYC

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
H [auth B],
I [auth C],
K [auth D],
E [auth A],
G [auth B],
H [auth B],
I [auth C],
K [auth D],
L [auth D]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
 Ligand Interaction
DBV
Query on DBV

Download Ideal Coordinates CCD File 
F [auth B],
J [auth D]
15,16-DIHYDROBILIVERDIN
C33 H36 N4 O6
ZQHDSLZHMAUUQK-ZTYGKHTCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.081α = 90
b = 132.081β = 90
c = 64.362γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata 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: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-07-16
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description