7QD1 | pdb_00007qd1

Structure of the orange carotenoid protein from Planktothrix agardhii binding echinenone in the P21 space group

• PDB DOI: https://doi.org/10.2210/pdb7QD1/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Planktothrix agardhii
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2021-11-26 Released: 2022-07-06 
• Deposition Author(s): Andreeva, E.A., Hartmann, E., Schlichting, I., Colletier, J.-P.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Structure-function-dynamics relationships in the peculiar Planktothrix PCC7805 OCP1: Impact of his-tagging and carotenoid type.

Wilson, A., Andreeva, E.A., Nizinski, S.J., Talbot, L., Hartmann, E., Schlichting, I., Burdzinski, G., Sliwa, M., Kirilovsky, D., Colletier, J.P.

(2022) Biochim Biophys Acta Bioenerg 1863: 148584-148584

• PubMed: 35752265 
• DOI: https://doi.org/10.1016/j.bbabio.2022.148584
• Primary Citation Related Structures: 
  7QCZ, 7QD0, 7QD1, 7QD2


• PubMed Abstract: 
  

  The orange carotenoid protein (OCP) is a photoactive protein involved in cyanobacterial photoprotection. Here, we report on the functional, spectral and structural characteristics of the peculiar Planktothrix PCC7805 OCP (Plankto-OCP). We show that this OCP variant is characterized by higher photoactivation and recovery rates, and a stronger energy-quenching activity, compared to other OCP studied thus far. We characterize the effect of the functionalizing carotenoid and of his-tagging on these reactions, and identify the time scales on which these modifications affect photoactivation. The presence of a his-tag at the C-terminus has a large influence on photoactivation, thermal recovery and PBS-fluorescence quenching, and likewise for the nature of the carotenoid that additionally affects the yield and characteristics of excited states and the ns-s dynamics of photoactivated OCP. By solving the structures of Plankto-OCP in the ECN- and CAN-functionalized states, each in two closely-related crystal forms, we further unveil the molecular breathing motions that animate Plankto-OCP at the monomer and dimer levels. We finally discuss the structural changes that could explain the peculiar properties of Plankto-OCP.

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Organizational Affiliation: 
• Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France; Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
Univ. Lille, CNRS, UMR 8516, LASIRE, LAboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, Lille 59000, France; Quantum Electronics Laboratory, Faculty of Physics, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, Poznan 61-614, Poland.
Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
Quantum Electronics Laboratory, Faculty of Physics, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, Poznan 61-614, Poland.
Univ. Lille, CNRS, UMR 8516, LASIRE, LAboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, Lille 59000, France. Electronic address: [e-mail].
Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France. Electronic address: [e-mail].
Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 71.81 kDa 
• Atom Count: 5,885 
• Modeled Residue Count: 621 
• Deposited Residue Count: 638 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orange carotenoid-binding protein	A, B [auth C]	319	Planktothrix agardhii	Mutation(s): 0  Gene Names: PLAM_2315
UniProt
Find proteins for A0A1J1JHR9 (Planktothrix agardhii) Explore A0A1J1JHR9  Go to UniProtKB:  A0A1J1JHR9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ECH (Subject of Investigation/LOI)	C [auth A], D [auth C]	beta,beta-caroten-4-one C40 H54 O QXNWZXMBUKUYMD-QQGJMDNJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.363	α = 90
b = 65.902	β = 102.354
c = 77.372	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-07-06 
Deposition Author(s): Andreeva, E.A., Hartmann, E., Schlichting, I., Colletier, J.-P.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-17-CE11-0018-01
Agence Nationale de la Recherche (ANR)	France	ANR-2018-CE11-0005-02
Agence Nationale de la Recherche (ANR)	France	ANR-10-INBS-05-02
Agence Nationale de la Recherche (ANR)	France	ANR-17-EURE-0003

Revision History  

• Version 1.0: 2022-07-06
  Type: Initial release
  
• Version 1.1: 2022-07-13
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary