8C69 | pdb_00008c69

Light SFX structure of D.m(6-4)photolyase at 100 microsecond time delay

• PDB DOI: https://doi.org/10.2210/pdb8C69/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-11 Released: 2023-11-01 
• Deposition Author(s): Cellini, A., Kumar, M., Nimmrich, A., Mutisya, J., Furrer, A., Beale, E.V., Carrillo, M., Malla, T.N., Maj, P., Dworkowskic, F., Cirelli, C., Ozerovi, D., Bacellar, C., Strandfuss, J., Weinert, T., Ihalainen, J.A., Yuan Wahlgren, W., Westenhoff, S.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.300 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.263 (Depositor), 0.263 (DCC) 
• R-Value Observed: 
  0.265 (Depositor) 

Starting Model: experimental

Literature

Directed ultrafast conformational changes accompany electron transfer in a photolyase as resolved by serial crystallography.

Cellini, A., Shankar, M.K., Nimmrich, A., Hunt, L.A., Monrroy, L., Mutisya, J., Furrer, A., Beale, E.V., Carrillo, M., Malla, T.N., Maj, P., Vrhovac, L., Dworkowski, F., Cirelli, C., Johnson, P.J.M., Ozerov, D., Stojkovic, E.A., Hammarstrom, L., Bacellar, C., Standfuss, J., Maj, M., Schmidt, M., Weinert, T., Ihalainen, J.A., Wahlgren, W.Y., Westenhoff, S.

(2024) Nat Chem 16: 624-632

• PubMed: 38225270 
• DOI: https://doi.org/10.1038/s41557-023-01413-9
• Primary Citation Related Structures: 
  8C1U, 8C69, 8C6A, 8C6B, 8C6C, 8C6F, 8C6H


• PubMed Abstract: 
  

  Charge-transfer reactions in proteins are important for life, such as in photolyases which repair DNA, but the role of structural dynamics remains unclear. Here, using femtosecond X-ray crystallography, we report the structural changes that take place while electrons transfer along a chain of four conserved tryptophans in the Drosophila melanogaster (6-4) photolyase. At femto- and picosecond delays, photoreduction of the flavin by the first tryptophan causes directed structural responses at a key asparagine, at a conserved salt bridge, and by rearrangements of nearby water molecules. We detect charge-induced structural changes close to the second tryptophan from 1 ps to 20 ps, identifying a nearby methionine as an active participant in the redox chain, and from 20 ps around the fourth tryptophan. The photolyase undergoes highly directed and carefully timed adaptations of its structure. This questions the validity of the linear solvent response approximation in Marcus theory and indicates that evolution has optimized fast protein fluctuations for optimal charge transfer.

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Organizational Affiliation: 
• Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.
Department of Chemistry, University of Washington, Seattle, WA, USA.
Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden.
Paul Scherrer Institut, Villigen, Switzerland.
Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
Department of Biology, Northeastern Illinois University, Chicago, IL, USA.
Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.
Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden.
Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden. [e-mail].
Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden. [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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 58.96 kDa 
• Atom Count: 4,292 
• Modeled Residue Count: 500 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cryptochrome-1	A	500	Drosophila melanogaster	Mutation(s): 0  Gene Names: phr6-4, CG2488
UniProt
Find proteins for Q8SXK5 (Drosophila melanogaster) Explore Q8SXK5  Go to UniProtKB:  Q8SXK5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.300 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.263 (Depositor), 0.263 (DCC) 
• R-Value Observed: 0.265 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.9	α = 90
b = 103.9	β = 90
c = 52.19	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-01 
Deposition Author(s): Cellini, A., Kumar, M., Nimmrich, A., Mutisya, J., Furrer, A., Beale, E.V., Carrillo, M., Malla, T.N., Maj, P., Dworkowskic, F., Cirelli, C., Ozerovi, D., Bacellar, C., Strandfuss, J., Weinert, T., Ihalainen, J.A., Yuan Wahlgren, W., Westenhoff, S.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	--

Revision History  

• Version 1.0: 2023-11-01
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Database references