9WZR | pdb_00009wzr

PmCas12m-crRNA-target DNA complex

• PDB DOI: https://doi.org/10.2210/pdb9WZR/pdb
• EM Map EMD-66405: EMDB EMDataResource
• NAKB: 9WZR

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


• Deposited: 2025-09-29 Released: 2026-09-23 
• Deposition Author(s): Meng, J., Tao, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure-guided discovery and engineering of miniature CRISPR-Cas12m for epigenome editing.

Yu, T., Ji, M., Yu, D., Guan, Z., Zhu, R., Jiang, Y., Yang, Z., Qiu, L., Zhang, Z., Mu, J., Mao, F., Xiang, K., Bai, L., Li, K.

(2026) Nat Struct Mol Biol 

• PubMed: 42749924 
• DOI: https://doi.org/10.1038/s41594-026-01890-9
• Primary Citation Related Structures: 
  9WZR


• PubMed Abstract: 
  

  CRISPR-based epigenome editing represents a programmable strategy to precisely modulate gene expression, holding promise for therapeutic applications. However, the large size of dCas proteins substantially impedes delivery using adeno-associated virus (AAV) vectors. Here, through iterative bioinformatics analysis, structure-guided predictions and functional assays, we identified and characterized a miniature subtype V-M CRISPR-Cas12m from Pelomicrobium methylotrophicum. PmCas12m exhibited flexible 5'-YTN-3' PAM-dependent recognition and robust double-stranded DNA-binding properties while lacking DNA cleavage activity, thus rendering it a valuable tool for epigenome editing. Cryo-electron microscopy structures of PmCas12m unveiled its molecular mechanism of target DNA binding. Guided by these structural insights, we used deep mutational scanning and protein engineering to develop xCas12m, a hypercompact variant with highly potent and specific epigenome-editing capabilities in human cells. We further constructed the xCas12m-CRISPRoff platform in a single AAV vector, which achieved durable epigenetic silencing and effective inhibition of hepatitis B virus infection in a mouse model. Collectively, these findings establish xCas12m as a versatile epigenome-editing platform with notable potential for treating diseases, paving the way for clinical translation of epigenetic therapies.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
Department of Biophysics, State Key Laboratory of Natural and Biomimetic Drug, School of Basic Medical Sciences, Peking University, Beijing, China.
Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China.
Cancer Center, Peking University Third Hospital, Beijing, China.
Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China. [e-mail].
Department of Biophysics, State Key Laboratory of Natural and Biomimetic Drug, School of Basic Medical Sciences, Peking University, Beijing, China. [e-mail].
Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China. [e-mail].

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: 107.84 kDa 
• Atom Count: 6,757 
• Modeled Residue Count: 684 
• Deposited Residue Count: 729 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transposase	A	601	Pelomicrobium methylotrophicum	Mutation(s): 0  Gene Names: FR698_00030
UniProt
Find proteins for A0A5C7EM61 (Pelomicrobium methylotrophicum) Explore A0A5C7EM61  Go to UniProtKB:  A0A5C7EM61

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA	B	56	Pelomicrobium methylotrophicum

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA(TS)	C	36	Pelomicrobium methylotrophicum

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA(NTS)	D	36	Pelomicrobium methylotrophicum

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-23 
Deposition Author(s): Meng, J., Tao, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171212

Revision History  

• Version 1.0: 2026-09-23
  Type: Initial release
  
• Version 1.1: 2026-09-30
  Changes: Data collection, Database references