8Z3X | pdb_00008z3x

SFX structure of CraCRY 30 us after photoexcitation of the oxidized protein

• PDB DOI: https://doi.org/10.2210/pdb8Z3X/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Chlamydomonas reinhardtii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-04-16 Released: 2025-05-14 
• Deposition Author(s): Maestre-Reyna, M., Hosokawa, Y., Wang, P.-H., Saft, M., Caramello, N., Engilberge, S., Franz-Badur, S., Ngura Putu, E.P.G., Nakamura, M., Wu, W.-J., Wu, H.-Y., Lee, C.-C., Huang, W.-C., Huang, K.-F., Chang, Y.-K., Yang, C.-H., Lin, W.-T., Yang, K.-C., Ban, Y., Imura, T., Kazuoka, A., Tanida, E., Owada, S., Joti, Y., Tanaka, R., Tanaka, T., Luo, F., Tono, K., Kiontke, S., Korf, L., Umena, Y., Tosha, T., Bessho, Y., Nango, E., Iwata, S., Royant, A., Tsai, M.-D., Yamamoto, J., Essen, L.-O.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan), Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Science and Technology, Japan Society for the Promotion of Science (JSPS), National Science Council (NSC, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Capturing structural intermediates in an animal-like cryptochrome photoreceptor by time-resolved crystallography.

Maestre-Reyna, M., Hosokawa, Y., Wang, P.H., Saft, M., Caramello, N., Engilberge, S., Franz-Badur, S., Gusti Ngurah Putu, E.P., Nakamura, M., Wu, W.J., Wu, H.Y., Lee, C.C., Huang, W.C., Huang, K.F., Chang, Y.K., Yang, C.H., Fong, M.I., Lin, W.T., Yang, K.C., Ban, Y., Imura, T., Kazuoka, A., Tanida, E., Owada, S., Joti, Y., Tanaka, R., Tanaka, T., Kang, J., Luo, F., Tono, K., Kiontke, S., Korf, L., Umena, Y., Tosha, T., Bessho, Y., Nango, E., Iwata, S., Royant, A., Tsai, M.D., Yamamoto, J., Essen, L.O.

(2025) Sci Adv 11: eadu7247-eadu7247

• PubMed: 40378212 
• DOI: https://doi.org/10.1126/sciadv.adu7247
• Primary Citation of Related Structures:  
  8Z1J, 8Z24, 8Z26, 8Z2D, 8Z3D, 8Z3G, 8Z3L, 8Z3X, 8Z41, 8Z44, 8Z45, 8Z4K, 8Z4M, 8Z4P, 8Z4U, 8Z6I, 8Z6J, 8Z6K, 8Z8F, 8Z8K, 8ZA8, 8ZLR


• PubMed Abstract: 
  

  Animal-like cryptochromes are photoreceptors that control circadian rhythm and signaling in many eukaryotes. Transient photoreduction of the cryptochrome flavin chromophore initiated signaling via a poorly understood mechanism. By serial femtosecond crystallography (SFX), we show that the photoreduction mechanism of Chlamydomonas reinhardtii cryptochrome involves three loci [carboxyl-terminal region, a transient protonation pathway, and flavin adenine dinucleotide (FAD)-binding site] acting in unison to accomplish three effects: radical pair stabilization, protonation of FAD radical, and formation of the signaling state. Using 19 time-resolved SFX snapshots between 10 nanoseconds and 233 milliseconds, we found that light-driven FAD ^•- /tyrosyl-373 radical pair (RP) formation primes α22 unfolding. Electron transfer-dependent protonation of aspartate-321 by tyrosine-373 is the epicenter of unfolding by disrupting salt bridges between α22 and the photolyase homology region. Before helix unfolding, another pathway opens transiently for FAD ^•- protonation and RP stabilization. This link between RP formation and conformational changes provides a structural basis for signaling by animal-like cryptochromes.

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Organizational Affiliation: 

Department of Chemistry, National Taiwan University, 1Roosevelt Rd. Sec. 4, Taipei 106, Taiwan.

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: 58.63 kDa 
• Atom Count: 4,209 
• Modeled Residue Count: 489 
• Deposited Residue Count: 509 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cryptochrome photoreceptor	A	509	Chlamydomonas reinhardtii	Mutation(s): 0  Gene Names: UVR3, CHLRE_06g278251v5, CHLREDRAFT_206002
UniProt
Find proteins for A8J8W0 (Chlamydomonas reinhardtii) Explore A8J8W0  Go to UniProtKB:  A8J8W0

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
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.84	α = 90
b = 65.6	β = 90
c = 153.13	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
pointless	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Maestre-Reyna, M., Hosokawa, Y., Wang, P.-H., Saft, M., Caramello, N., Engilberge, S., Franz-Badur, S., Ngura Putu, E.P.G., Nakamura, M., Wu, W.-J., Wu, H.-Y., Lee, C.-C., Huang, W.-C., Huang, K.-F., Chang, Y.-K., Yang, C.-H., Lin, W.-T., Yang, K.-C., Ban, Y., Imura, T., Kazuoka, A., Tanida, E., Owada, S., Joti, Y., Tanaka, R., Tanaka, T., Luo, F., Tono, K., Kiontke, S., Korf, L., Umena, Y., Tosha, T., Bessho, Y., Nango, E., Iwata, S., Royant, A., Tsai, M.-D., Yamamoto, J., Essen, L.-O.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	AS-KPQ-105-TPP
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	AS-KPQ-109-TPP2
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP20H05442
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP22H04751
Japan Science and Technology	Japan	JPMJFR2057
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H05776
National Science Council (NSC, Taiwan)	Taiwan	111-2113-M-002-029-MY3
Japan Society for the Promotion of Science (JSPS)	Japan	JP21J13329

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release
  
• Version 1.1: 2025-05-28
  Changes: Database references