8RJS

Serial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in I5 intermediate state.

Summary for 8RJS

• Entry DOI: 10.2210/pdb8rjs/pdb
• Related: 6G1Y 6G1Z 6G20 8RJM 8RJN 8RJO 8RJP 8RJQ 8RJR 8RJT 8RJU
• Descriptor: histidine kinase, 3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid, SULFATE ION, ... (5 entities in total)
• Functional Keywords: fluorescent protein, phytochrome, bacteriophytochrome, intermediate, optogenetic, signaling protein
• Biological source: Agrobacterium fabrum str. C58
• Total number of polymer chains: 2
• Total formula weight: 116700.06

Authors

Sauthof, L.,Schmidt, A.,Szczepek, M.,Brewster, A.S.,Kern, J.F.,Scheerer, P. (deposition date: 2023-12-21, release date: 2025-05-14, Last modification date: 2025-06-11)

Primary citation

Sauthof, L.,Szczepek, M.,Schmidt, A.,Bhowmick, A.,Dasgupta, M.,Mackintosh, M.J.,Gul, S.,Fuller, F.D.,Chatterjee, R.,Young, I.D.,Michael, N.,Heyder, N.A.,Bauer, B.,Koch, A.,Bogacz, I.,Kim, I.S.,Simon, P.S.,Butryn, A.,Aller, P.,Chukhutsina, V.U.,Baxter, J.M.,Hutchison, C.D.M.,Liebschner, D.,Poon, B.,Sauter, N.K.,Miller, M.D.,Alonso-Mori, R.,Hunter, M.S.,Batyuk, A.,Owada, S.,Tono, K.,Tanaka, R.,van Thor, J.J.,Krauss, N.,Lamparter, T.,Brewster, A.S.,Schapiro, I.,Orville, A.M.,Yachandra, V.K.,Yano, J.,Hildebrandt, P.,Kern, J.F.,Scheerer, P.
Serial-femtosecond crystallography reveals how a phytochrome variant couples chromophore and protein structural changes.
Sci Adv, 11:eadp2665-eadp2665, 2025

PubMed Abstract: The photoreaction and commensurate structural changes of a chromophore within biological photoreceptors elicit conformational transitions of the protein promoting the switch between deactivated and activated states. We investigated how this coupling is achieved in a bacterial phytochrome variant, Agp2-PAiRFP2. Contrary to classical protein crystallography, which only allows probing (cryo-trapped) stable states, we have used time-resolved serial femtosecond x-ray crystallography (tr-SFX) and pump-probe techniques with various illumination and delay times with respect to photoexcitation of the parent Pfr state. Thus, structural data for seven time frames were sorted into groups of molecular events along the reaction coordinate. They range from chromophore isomerization to the formation of Meta-F, the intermediate that precedes the functional relevant secondary structure transition of the tongue. Structural data for the early events were used to calculate the photoisomerization pathway to complement the experimental data. Late events allow identifying the molecular switch that is linked to the intramolecular proton transfer as a prerequisite for the following structural transitions.

PubMed: 40435264
DOI: 10.1126/sciadv.adp2665

Experimental method

X-RAY DIFFRACTION (2.43 Å)