6XMF | pdb_00006xmf

Cryo-EM structure of Cas12g binary complex

• PDB DOI: https://doi.org/10.2210/pdb6XMF/pdb
• NAKB: 6XMF
• EM Map EMD-22257: EMDB EMDataResource

• Classification: HYDROLASE/RNA
• Organism(s): metagenome
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-06-30 Released: 2021-01-13 
• Deposition Author(s): Chang, L., Li, Z., Zhang, H.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of the RNA-guided ribonuclease Cas12g.

Li, Z., Zhang, H., Xiao, R., Han, R., Chang, L.

(2021) Nat Chem Biol 17: 387-393

• PubMed: 33495647 
• DOI: https://doi.org/10.1038/s41589-020-00721-2
• Primary Citation Related Structures: 
  6XMF, 6XMG


• PubMed Abstract: 
  

  Cas12g, the type V-G CRISPR-Cas effector, is an RNA-guided ribonuclease that targets single-stranded RNA substrate. The CRISPR-Cas12g system offers a potential platform for transcriptome engineering and diagnostic applications. We determined the structures of Cas12g-guide RNA complexes in the absence and presence of target RNA by cryo-EM to a resolution of 3.1 Å and 4.8 Å, respectively. Cas12g adopts a bilobed structure with miniature REC2 and Nuc domains, whereas the guide RNAs fold into a flipped 'F' shape, which is primarily recognized by the REC lobe. Target RNA and the CRISPR RNA (crRNA) guide form a duplex that inserts into the central cavity between the REC and NUC lobes, inducing conformational changes in both lobes to activate Cas12g. The structural insights would facilitate the development of Cas12g-based applications.

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Organizational Affiliation: 
• Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
Department of Biological Sciences, Purdue University, West Lafayette, IN, USA. [e-mail].
Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 129.31 kDa 
• Atom Count: 7,382 
• Modeled Residue Count: 736 
• Deposited Residue Count: 889 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-Cas	A	767	metagenome	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (116-MER)	B [auth C]	122	metagenome

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.0

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Chang, L., Li, Z., Zhang, H.

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2021-02-03
  Changes: Database references
• Version 1.2: 2021-02-10
  Changes: Database references
• Version 1.3: 2021-04-07
  Changes: Database references
• Version 1.4: 2023-05-10
  Changes: Database references, Source and taxonomy
• Version 1.5: 2023-06-07
  Changes: Source and taxonomy, Structure summary
• Version 1.6: 2024-05-15
  Changes: Data collection
• Version 1.7: 2025-05-28
  Changes: Data collection, Structure summary