9J09 | pdb_00009j09

Cryo-EM structure of the RdCas12n-sgRNA-DNA complex

• PDB DOI: https://doi.org/10.2210/pdb9J09/pdb
• NAKB: 9J09
• EM Map EMD-61051: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN/DNA/RNA
• Organism(s): Rothia dentocariosa, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-02 Released: 2025-06-04 
• Deposition Author(s): Fu, W., Ji, Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

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

Literature

Mechanisms and engineering of a miniature type V-N CRISPR-Cas12 effector enzyme

Fu, W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 147.13 kDa 
• Atom Count: 5,227 
• Modeled Residue Count: 407 
• Deposited Residue Count: 808 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transposase	A	540	Rothia dentocariosa	Mutation(s): 0  Gene Names: HXO56_11955
UniProt
Find proteins for A0A7D4LAR1 (Rothia dentocariosa) Explore A0A7D4LAR1  Go to UniProtKB:  A0A7D4LAR1

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	B [auth C]	40	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*CP*TP*GP*TP*GP*AP*GP*AP*AP*AP*CP*CP*G)-3')	C [auth D]	14	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
sgRNA	D [auth R]	214	Rothia dentocariosa

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: 2025-06-04 
Deposition Author(s): Fu, W., Ji, Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21922705
National Natural Science Foundation of China (NSFC)	China	2207783
National Natural Science Foundation of China (NSFC)	China	91753127

Revision History  

• Version 1.0: 2025-06-04
  Type: Initial release