9N9M | pdb_00009n9m

Cryo-EM structure of the dCas12f-gRNA-DNA complex (partial R-Loop)

• PDB DOI: https://doi.org/10.2210/pdb9N9M/pdb
• EM Map EMD-49173: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN/DNA/RNA
• Organism(s): Flagellimonas taeanensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-02-11 Released: 2025-12-24 
• Deposition Author(s): Chang, L., Sternberg, S.H., Xiao, R., Hoffmann, F.T., Wiegand, T., Xie, D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), The Pew Charitable Trusts

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of RNA-guided transcription via Cas12f-Sigma factor association

Renjian, X., Leifu, C.

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: electron microscopy

Macromolecule Content 

• Total Structure Weight: 152.73 kDa 
• Atom Count: 7,995 
• Modeled Residue Count: 811 
• Deposited Residue Count: 943 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease-deactivated Cas12f	A, B	365	Flagellimonas taeanensis	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA non-template strand	C [auth a]	60	Flagellimonas taeanensis

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA template strand	D [auth b]	60	Flagellimonas taeanensis

Entity ID: 4
Molecule	Chains	Length	Organism	Image
gRNA (76-MER)	E [auth c]	93	Flagellimonas taeanensis

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Chang, L., Sternberg, S.H., Xiao, R., Hoffmann, F.T., Wiegand, T., Xie, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM138675
National Science Foundation (NSF, United States)	United States	2339799
National Science Foundation (NSF, United States)	United States	2239685
The Pew Charitable Trusts	United States	--

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release