9MTY | pdb_00009mty

Structure of TIGR-TasR in complex with tigRNA and target DNA after DNA cleavage

• PDB DOI: https://doi.org/10.2210/pdb9MTY/pdb
• NAKB: 9MTY
• EM Map EMD-48616: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN/RNA/DNA
• Organism(s): Thermoproteota archaeon, Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-12 Released: 2025-03-05 
• Deposition Author(s): Wilkinson, M.E., Zhang, F.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.05 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

TIGR-Tas: A family of modular RNA-guided DNA-targeting systems in prokaryotes and their viruses.

Faure, G., Saito, M., Wilkinson, M.E., Quinones-Olvera, N., Xu, P., Flam-Shepherd, D., Kim, S., Reddy, N., Zhu, S., Evgeniou, L., Koonin, E.V., Macrae, R.K., Zhang, F.

(2025) Science 388: eadv9789-eadv9789

• PubMed: 40014690 
• DOI: https://doi.org/10.1126/science.adv9789
• Primary Citation of Related Structures:  
  9MTY


• PubMed Abstract: 
  

  RNA-guided systems provide remarkable versatility, enabling diverse biological functions. Through iterative structural and sequence homology-based mining starting with a guide RNA-interaction domain of Cas9, we identified a family of RNA-guided DNA-targeting proteins in phage and parasitic bacteria. Each system consists of a Tandem Interspaced Guide RNA (TIGR) array and a TIGR-associated (Tas) protein containing a Nop domain, sometimes fused to HNH (TasH) or RuvC (TasR) nuclease domains. We show that TIGR arrays are processed into 36-nt RNAs (tigRNAs) that direct sequence-specific DNA binding through a tandem-spacer targeting mechanism. TasR can be reprogrammed for precise DNA cleavage, including in human cells. The structure of TasR reveals striking similarities to box C/D snoRNPs and IS110 RNA-guided transposases, providing insights into the evolution of diverse RNA-guided systems.

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Organizational Affiliation: 
• Broad Institute of MIT and Harvard, Cambridge, MA, USA.
McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.
Department of Brain and Cognitive Science, MIT, Cambridge, MA, USA.
Department of Biological Engineering, MIT, Cambridge, MA, USA.
Howard Hughes Medical Institute, Cambridge, MA, USA.
Department of Systems Biology, Harvard University, Boston, MA, USA.
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 125.03 kDa 
• Atom Count: 7,106 
• Modeled Residue Count: 698 
• Deposited Residue Count: 818 
• Unique protein chains: 1
• Unique nucleic acid chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transposase IS116/IS110/IS902 C-terminal domain-containing protein	A, B	331	Thermoproteota archaeon	Mutation(s): 0  Gene Names: DWQ19_11745

Entity ID: 2
Molecule	Chains	Length	Organism	Image
tigRNA	C	36	Thermoproteota archaeon

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Target DNA, spacer A targeted strand, 5' of cut	D	34	Escherichia coli

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Target DNA, spacer A targeted strand, 3' of cut	E [auth F]	26	Escherichia coli

Entity ID: 5
Molecule	Chains	Length	Organism	Image
Target DNA, spacer B targeted strand, 5' of cut	F [auth E]	34	Escherichia coli

Entity ID: 6
Molecule	Chains	Length	Organism	Image
Target DNA, spacer B targeted strand, 3' of cut	G	26	Escherichia coli

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	H [auth A], I [auth A], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.05 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	5.0
MODEL REFINEMENT	Coot
MODEL REFINEMENT	ISOLDE
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-05 
Deposition Author(s): Wilkinson, M.E., Zhang, F.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2025-03-05
  Type: Initial release
  
• Version 1.1: 2025-04-16
  Changes: Data collection, Database references
• Version 1.2: 2025-05-14
  Changes: Data collection, Database references