4XB4 | pdb_00004xb4

Structure of the N-terminal domain of OCP binding canthaxanthin

• PDB DOI: https://doi.org/10.2210/pdb4XB4/pdb

• Classification: Carotenoid binding protein
• Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-12-16 Released: 2015-07-15 
• Deposition Author(s): Kerfeld, C.A., Sutter, M., Leverenz, R.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

PHOTOSYNTHESIS. A 12 angstrom carotenoid translocation in a photoswitch associated with cyanobacterial photoprotection.

Leverenz, R.L., Sutter, M., Wilson, A., Gupta, S., Thurotte, A., Bourcier de Carbon, C., Petzold, C.J., Ralston, C., Perreau, F., Kirilovsky, D., Kerfeld, C.A.

(2015) Science 348: 1463-1466

• PubMed: 26113721 
• DOI: https://doi.org/10.1126/science.aaa7234
• Primary Citation Related Structures: 
  4XB4, 4XB5


• PubMed Abstract: 
  

  Pigment-protein and pigment-pigment interactions are of fundamental importance to the light-harvesting and photoprotective functions essential to oxygenic photosynthesis. The orange carotenoid protein (OCP) functions as both a sensor of light and effector of photoprotective energy dissipation in cyanobacteria. We report the atomic-resolution structure of an active form of the OCP consisting of the N-terminal domain and a single noncovalently bound carotenoid pigment. The crystal structure, combined with additional solution-state structural data, reveals that OCP photoactivation is accompanied by a 12 angstrom translocation of the pigment within the protein and a reconfiguration of carotenoid-protein interactions. Our results identify the origin of the photochromic changes in the OCP triggered by light and reveal the structural determinants required for interaction with the light-harvesting antenna during photoprotection.

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Organizational Affiliation: 
• MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA. Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Commissariat à l'Energie Atomique (CEA), Institut de Biologie et Technologies de Saclay (iBiTec-S), 91191 Gif-sur-Yvette, France. Centre National de la Recherche Scientifique (CNRS), I2BC, UMR 9198, 91191 Gif-sur-Yvette, France.
Berkeley Center for Structural Biology, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France.
MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA. Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.34 kDa 
• Atom Count: 2,644 
• Modeled Residue Count: 282 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orange carotenoid-binding protein	A, B	152	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0  Gene Names: slr1963
UniProt
Find proteins for P74102 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P74102  Go to UniProtKB:  P74102

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
45D	C [auth A], D [auth B]	beta,beta-carotene-4,4'-dione C40 H52 O2 FDSDTBUPSURDBL-DKLMTRRASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.251	α = 90
b = 64.112	β = 114.89
c = 53.634	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-15 
Deposition Author(s): Kerfeld, C.A., Sutter, M., Leverenz, R.L.

Revision History  

• Version 1.0: 2015-07-15
  Type: Initial release
  
• Version 1.1: 2015-09-09
  Changes: Data collection
• Version 1.2: 2015-12-30
  Changes: Non-polymer description
• Version 1.3: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description