7XF0 | pdb_00007xf0

Crystal strucutre of CasDinG in complex with ATP

• PDB DOI: https://doi.org/10.2210/pdb7XF0/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-03-31 Released: 2023-07-26 
• Deposition Author(s): Zhang, J.T., Cui, N., Liu, Y.R., Huang, H.D., Jia, N.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.261 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Type IV-A CRISPR-Csf complex: Assembly, dsDNA targeting, and CasDinG recruitment.

Cui, N., Zhang, J.T., Liu, Y., Liu, Y., Liu, X.Y., Wang, C., Huang, H., Jia, N.

(2023) Mol Cell 83: 2493-2508.e5

• PubMed: 37343553 
• DOI: https://doi.org/10.1016/j.molcel.2023.05.036
• Primary Citation Related Structures: 
  7XEX, 7XF0, 7XF1, 7XFZ, 7XG0, 7XG2, 7XG3, 7XG4


• PubMed Abstract: 
  

  Type IV CRISPR-Cas systems, which are primarily found on plasmids and exhibit a strong plasmid-targeting preference, are the only one of the six known CRISPR-Cas types for which the mechanistic details of their function remain unknown. Here, we provide high-resolution functional snapshots of type IV-A Csf complexes before and after target dsDNA binding, either in the absence or presence of CasDinG, revealing the mechanisms underlying Csf ^crRNA complex assembly, "DWN" PAM-dependent dsDNA targeting, R-loop formation, and CasDinG recruitment. Furthermore, we establish that CasDinG, a signature DinG family helicase, harbors ssDNA-stimulated ATPase activity and ATP-dependent 5'-3' DNA helicase activity. In addition, we show that CasDinG unwinds the non-target strand (NTS) and target strand (TS) of target dsDNA from the Csf ^crRNA complex. These molecular details advance our mechanistic understanding of type IV-A CRISPR-Csf function and should enable Csf complexes to be harnessed as genome-engineering tools for biotechnological applications.

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Organizational Affiliation: 
• Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China.
Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
Faculty of Pharmaceutical Sciences, Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen 518055, China; Center for Human Tissues and Organs Degeneration, Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen 518055, China.
Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China. Electronic address: [e-mail].
Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; Shenzhen Key Laboratory of Cell Microenvironment, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China; Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, China. Electronic address: [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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 205.34 kDa 
• Atom Count: 13,697 
• Modeled Residue Count: 1,782 
• Deposited Residue Count: 1,878 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CasDinG	A [auth C], B [auth A], C [auth B]	626	Pseudomonas aeruginosa	Mutation(s): 0
UniProt
Find proteins for A0AA82WNX9 (Pseudomonas aeruginosa) Explore A0AA82WNX9  Go to UniProtKB:  A0AA82WNX9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	D [auth C], E [auth A], F [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.261 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.546	α = 90
b = 72.095	β = 90.84
c = 224.23	γ = 90

Software Package:

Software Name	Purpose
DIALS	data scaling
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-26 
Deposition Author(s): Zhang, J.T., Cui, N., Liu, Y.R., Huang, H.D., Jia, N.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-07-26
  Type: Initial release
  
• Version 1.1: 2023-08-02
  Changes: Database references
• Version 1.2: 2024-05-29
  Changes: Data collection
• Version 1.3: 2026-03-04
  Changes: Refinement description, Structure summary