8J3R

Cryo-EM structure of the AsCas12f-HKRA-sgRNAS3-5v7-target DNA

• PDB DOI: https://doi.org/10.2210/pdb8J3R/pdb
• NAKB: 8J3R
• EM Map EMD-35965: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN/DNA/RNA
• Organism(s): Sulfoacidibacillus thermotolerans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-04-18 Released: 2023-09-27 
• Deposition Author(s): Hino, T., Omura, N.S., Nakagawa, R., Togashi, T., Takeda, N.S., Hiramoto, T., Tasaka, S., Hirano, H., Tokuyama, T., Uosaki, H., Ishiguro, H., Yamano, H., Ozaki, Y., Motooka, D., Mori, H., Kirita, Y., Kise, Y., Itoh, Y., Matoba, S., Aburatani, H., Yachie, N., Siksnys, V., Ohmori, T., Hoshino, A., Nureki, O.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.95 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Minimal and most efficient genome editing Cas enzyme

Hino, T., Omura, N.S., Nakagawa, R., Togashi, T., Takeda, N.S., Hiramoto, T., Tasaka, S., Hirano, H., Tokuyama, T., Uosaki, H., Ishiguro, H., Yamano, H., Ozaki, Y., Motooka, D., Mori, H., Kirita, Y., Kise, Y., Itoh, Y., Matoba, S., Aburatani, H., Yachie, N., Siksnys, V., Ohmori, T., Hoshino, A., Nureki, O.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 161.47 kDa 
• Atom Count: 9,526 
• Modelled Residue Count: 949 
• Deposited Residue Count: 1,057 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transposase IS605 OrfB C-terminal domain-containing protein	A, E [auth B]	432	Sulfoacidibacillus thermotolerans	Mutation(s): 4  Gene Names: BM613_13600
UniProt
Find proteins for A0A2U3D0N8 (Sulfoacidibacillus thermotolerans) Explore A0A2U3D0N8  Go to UniProtKB:  A0A2U3D0N8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (37-MER)	B [auth D]	37	Sulfoacidibacillus thermotolerans

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (38-MER)	C [auth E]	38	Sulfoacidibacillus thermotolerans

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (118-MER)	D [auth C]	118	Sulfoacidibacillus thermotolerans

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	G [auth A], H [auth C], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.95 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-27 
Deposition Author(s): Hino, T., Omura, N.S., Nakagawa, R., Togashi, T., Takeda, N.S., Hiramoto, T., Tasaka, S., Hirano, H., Tokuyama, T., Uosaki, H., Ishiguro, H., Yamano, H., Ozaki, Y., Motooka, D., Mori, H., Kirita, Y., Kise, Y., Itoh, Y., Matoba, S., Aburatani, H., Yachie, N., Siksnys, V., Ohmori, T., Hoshino, A., Nureki, O.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History  

• Version 1.0: 2023-09-27
  Type: Initial release