4LMX

Light harvesting complex PE555 from the cryptophyte Hemiselmis andersenii CCMP644

• PDB DOI:  https://doi.org/10.2210/pdb4LMX/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Hemiselmis andersenii
• Mutation(s): Yes 


• Deposited: 2013-07-11 Released: 2014-06-18 
• Deposition Author(s): Harrop, S.J., Wilk, K.E., Curmi, P.M.G.

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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 

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

• PubMed: 24979784 
• DOI: https://doi.org/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. 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.

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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 [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 166.48 kDa 
• Atom Count: 14,008 
• Modelled Residue Count: 1,473 
• Deposited Residue Count: 1,487 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cryptophyte phycoerythrin (alpha-2 chain)	A	62	Hemiselmis andersenii	Mutation(s): 0  Gene Names: HAND1043_LOCUS7931
UniProt
Find proteins for U5TBJ3 (Hemiselmis andersenii) Explore U5TBJ3  Go to UniProtKB:  U5TBJ3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cryptophyte phycoerythrin (beta chain)	B, D, F, H, J, L	177	Hemiselmis andersenii	Mutation(s): 0
UniProt
Find proteins for U5T8W0 (Hemiselmis andersenii) Explore U5T8W0  Go to UniProtKB:  U5T8W0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
cryptophyte phycoerythrin (alpha-1 chain)	C	67	Hemiselmis andersenii	Mutation(s): 0
UniProt
Find proteins for U5TBU5 (Hemiselmis andersenii) Explore U5TBU5  Go to UniProtKB:  U5TBU5

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
cryptophyte phycoerythrin (alpha-1/alpha-2 chain)	E, G, I, K	67	Hemiselmis andersenii	Mutation(s): 7  Gene Names: HAND1043_LOCUS7931
UniProt
Find proteins for U5TBJ3 (Hemiselmis andersenii) Explore U5TBJ3  Go to UniProtKB:  U5TBJ3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEB	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
DBV	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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LYZ	A	L-PEPTIDE LINKING	C6 H14 N2 O3		LYS

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 = 66.073	α = 90
b = 76.741	β = 92.86
c = 142.593	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-18 
Deposition Author(s): Harrop, S.J., Wilk, K.E., Curmi, P.M.G.

Revision History  

• Version 1.0: 2014-06-18
  Type: Initial release
  
• Version 1.1: 2014-07-16
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description