4LMX

Light harvesting complex PE555 from the cryptophyte Hemiselmis andersenii CCMP644


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.161 

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Ligand Structure Quality Assessment 


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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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cryptophyte phycoerythrin (alpha-2 chain)A62Hemiselmis anderseniiMutation(s): 0 
Gene Names: HAND1041_18069HAND1043_LOCUS7937
UniProt
Find proteins for U5TBJ3 (Hemiselmis andersenii)
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Go to UniProtKB:  U5TBJ3
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cryptophyte phycoerythrin (beta chain)B, D, F, H, J, L177Hemiselmis anderseniiMutation(s): 0 
UniProt
Find proteins for U5T8W0 (Hemiselmis andersenii)
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
cryptophyte phycoerythrin (alpha-1 chain)C67Hemiselmis anderseniiMutation(s): 0 
UniProt
Find proteins for U5TBU5 (Hemiselmis andersenii)
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Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
cryptophyte phycoerythrin (alpha-1/alpha-2 chain)E, G, I, K67Hemiselmis anderseniiMutation(s): 7 
Gene Names: HAND1041_18069HAND1043_LOCUS7937
UniProt
Find proteins for U5TBJ3 (Hemiselmis andersenii)
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Go to UniProtKB:  U5TBJ3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEB (Subject of Investigation/LOI)
Query on PEB

Download Ideal Coordinates CCD File 
AA [auth H] , BA [auth H] , CA [auth I] , EA [auth J] , FA [auth J] , GA [auth K] , IA [auth L] , JA [auth L] , 
AA [auth H], BA [auth H], CA [auth I], EA [auth J], FA [auth J], GA [auth K], IA [auth L], JA [auth L], M [auth A], O [auth B], P [auth B], Q [auth C], S [auth D], T [auth D], U [auth E], W [auth F], X [auth F], Y [auth G]
PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-N
 Ligand Interaction
DBV (Subject of Investigation/LOI)
Query on DBV

Download Ideal Coordinates CCD File 
DA [auth J], HA [auth L], N [auth B], R [auth D], V [auth F], Z [auth H]15,16-DIHYDROBILIVERDIN
C33 H36 N4 O6
ZQHDSLZHMAUUQK-ZTYGKHTCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LYZ
Query on LYZ
AL-PEPTIDE LINKINGC6 H14 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.073α = 90
b = 76.741β = 92.86
c = 142.593γ = 90
Software Package:
Software NamePurpose
BLUEdata 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