7YD6

TR-SFX MmCPDII-DNA complex: 650 ps snapshot. Includes 650ps, dark, and extrapolated structure factors

• PDB DOI: https://doi.org/10.2210/pdb7YD6/pdb
• NAKB: 7YD6

• Classification: DNA BINDING PROTEIN
• Organism(s): Methanosarcina mazei Go1, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-07-04 Released: 2023-11-22 
• Deposition Author(s): Maestre-Reyna, M., Wang, P.-H., Nango, E., Hosokawa, Y., Saft, M., Furrer, A., Yang, C.-H., Ngura Putu, E.P.G., Wu, W.-J., Emmerich, H.-J., Engilberge, S., Caramello, N., Wranik, M., Glover, H.L., Franz-Badur, S., Wu, H.-Y., Lee, C.-C., Huang, W.-C., Huang, K.-F., Chang, Y.-K., Liao, J.-H., Weng, J.-H., Gad, W., Chang, C.-W., Pang, A.H., Gashi, D., Beale, E., Ozerov, D., Milne, C., Cirelli, C., Bacellar, C., Sugahara, M., Owada, S., Joti, Y., Yamashita, A., Tanaka, R., Tanaka, T., Luo, F.J., Tono, K., Kiontke, S., Spadaccini, R., Royant, A., Yamamoto, J., Iwata, S., Standfuss, J., Essen, L.-O., Bessho, Y., Tsai, M.-D.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan), Japan Society for the Promotion of Science (JSPS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.239 
• R-Value Work: 0.216 
• R-Value Observed: 0.217 

Literature

Visualizing the DNA repair process by a photolyase at atomic resolution.

Maestre-Reyna, M., Wang, P.H., Nango, E., Hosokawa, Y., Saft, M., Furrer, A., Yang, C.H., Gusti Ngurah Putu, E.P., Wu, W.J., Emmerich, H.J., Caramello, N., Franz-Badur, S., Yang, C., Engilberge, S., Wranik, M., Glover, H.L., Weinert, T., Wu, H.Y., Lee, C.C., Huang, W.C., Huang, K.F., Chang, Y.K., Liao, J.H., Weng, J.H., Gad, W., Chang, C.W., Pang, A.H., Yang, K.C., Lin, W.T., Chang, Y.C., Gashi, D., Beale, E., Ozerov, D., Nass, K., Knopp, G., Johnson, P.J.M., Cirelli, C., Milne, C., Bacellar, C., Sugahara, M., Owada, S., Joti, Y., Yamashita, A., Tanaka, R., Tanaka, T., Luo, F., Tono, K., Zarzycka, W., Muller, P., Alahmad, M.A., Bezold, F., Fuchs, V., Gnau, P., Kiontke, S., Korf, L., Reithofer, V., Rosner, C.J., Seiler, E.M., Watad, M., Werel, L., Spadaccini, R., Yamamoto, J., Iwata, S., Zhong, D., Standfuss, J., Royant, A., Bessho, Y., Essen, L.O., Tsai, M.D.

(2023) Science 382: eadd7795-eadd7795

• PubMed: 38033054 
• DOI: https://doi.org/10.1126/science.add7795
• Primary Citation of Related Structures:  
  7YC7, 7YCM, 7YCP, 7YCR, 7YD6, 7YD7, 7YD8, 7YDZ, 7YE0, 7YEB, 7YEC, 7YEE, 7YEI, 7YEJ, 7YEK, 7YEL, 7YEM, 8KCM


• PubMed Abstract: 
  

  Photolyases, a ubiquitous class of flavoproteins, use blue light to repair DNA photolesions. In this work, we determined the structural mechanism of the photolyase-catalyzed repair of a cyclobutane pyrimidine dimer (CPD) lesion using time-resolved serial femtosecond crystallography (TR-SFX). We obtained 18 snapshots that show time-dependent changes in four reaction loci. We used these results to create a movie that depicts the repair of CPD lesions in the picosecond-to-nanosecond range, followed by the recovery of the enzymatic moieties involved in catalysis, completing the formation of the fully reduced enzyme-product complex at 500 nanoseconds. Finally, back-flip intermediates of the thymine bases to reanneal the DNA were captured at 25 to 200 microseconds. Our data cover the complete molecular mechanism of a photolyase and, importantly, its chemistry and enzymatic catalysis at work across a wide timescale and at atomic resolution.

---

Organizational Affiliation: 

Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 129.04 kDa 
• Atom Count: 8,502 
• Modelled Residue Count: 938 
• Deposited Residue Count: 1,018 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribodipyrimidine photo-lyase	A, B	482	Methanosarcina mazei Go1	Mutation(s): 1  Gene Names:  DU34_19720, DU35_15210, DU36_16165, DU37_08235, DU38_17340, DU39_00605, DU41_17975, DU42_05505, DU44_19145, DU46_16260, DU48_13210, DU49_01325, DU51_15440, DU57_04540, DU59_03190, DU60_01690, DU61_08490, DU62_04430, DU63_10745, DU65_18915, DU69_04700, DU71_05355, DU72_08110, DU74_09110, FQU78_02295 EC: 4.1.99.3
UniProt
Find proteins for Q8PYK9 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PYK9  Go to UniProtKB:  Q8PYK9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
CPD photolesion containing DNA	C, E	13	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
complementary oligonucleotide to the CPD containing DNA	D, F	14	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	G [auth A], I [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SO4	H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.239 
• R-Value Work: 0.216 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.47	α = 90
b = 115.93	β = 90
c = 169.35	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: 2023-11-22 
Deposition Author(s): Maestre-Reyna, M., Wang, P.-H., Nango, E., Hosokawa, Y., Saft, M., Furrer, A., Yang, C.-H., Ngura Putu, E.P.G., Wu, W.-J., Emmerich, H.-J., Engilberge, S., Caramello, N., Wranik, M., Glover, H.L., Franz-Badur, S., Wu, H.-Y., Lee, C.-C., Huang, W.-C., Huang, K.-F., Chang, Y.-K., Liao, J.-H., Weng, J.-H., Gad, W., Chang, C.-W., Pang, A.H., Gashi, D., Beale, E., Ozerov, D., Milne, C., Cirelli, C., Bacellar, C., Sugahara, M., Owada, S., Joti, Y., Yamashita, A., Tanaka, R., Tanaka, T., Luo, F.J., Tono, K., Kiontke, S., Spadaccini, R., Royant, A., Yamamoto, J., Iwata, S., Standfuss, J., Essen, L.-O., Bessho, Y., Tsai, M.-D.

---

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
Japan Society for the Promotion of Science (JSPS)	Japan	16K01942

Revision History  

• Version 1.0: 2023-11-22
  Type: Initial release
  
• Version 1.1: 2023-12-13
  Changes: Database references
• Version 1.2: 2024-03-13
  Changes: Source and taxonomy