9LKJ | pdb_00009lkj

Structure of Cas9-sgRNA-A27

• PDB DOI: https://doi.org/10.2210/pdb9LKJ/pdb
• NAKB: 9LKJ
• EM Map EMD-63180: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Streptococcus pyogenes, Streptococcus pyogenes serotype M1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-16 Released: 2026-01-21 
• Deposition Author(s): Yu, L., Zhu, Y., Lu, Z., Huang, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.68 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

An anti-CRISPR targets the sgRNA to block Cas9 and guides the design of enhanced genome editors.

Yu, L., Yin, M., Zhu, Y., Lu, Z., Xiao, B., Zhou, F., Yu, Y., Huang, Z.

(2026) Nat Struct Mol Biol 33: 318-329

• PubMed: 41555077 
• DOI: https://doi.org/10.1038/s41594-025-01741-z
• Primary Citation Related Structures: 
  9LKJ


• PubMed Abstract: 
  

  Bacteriophages have evolved anti-CRISPR (Acr) proteins to combat the adaptive immunity provided by bacterial CRISPR-Cas systems. Here, we report the cryo-electron microscopy structure of an anti-Cas9 protein AcrIIA27 bound to SpyCas9-sgRNA (single guide RNA) complex. Our structure reveals that AcrIIA27 binds the solvent-exposed phosphate backbone of the sgRNA, acting as a potent inhibitor of diverse Cas9 orthologs. AcrIIA27 in the structure is positioned near the protospacer-adjacent motif DNA-binding pocket on SpyCas9, causing steric hindrance that prevents substrate DNA recognition. This mechanism suggests solvent-exposed regions of sgRNAs (PTP RNAs), prone to nonspecific binding of positively charged components, may compromise CRISPR-Cas genome-editing efficiency. Indeed, truncations of the PTP RNAs in different editing systems significantly enhance genome-editing efficiency in human cells. Overall, our findings reveal a previously uncharacterized inhibition mechanism of an anti-Cas protein and offers a general strategy for developing more efficient genome-editing tools.

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Organizational Affiliation: 
• HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.
Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China. [e-mail].
Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China. [e-mail].
New Cornerstone Science Institute, Harbin Institute of Technology, Harbin, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 197.97 kDa 
• Atom Count: 11,645 
• Modeled Residue Count: 1,380 
• Deposited Residue Count: 1,539 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage protein	A	79	Streptococcus pyogenes	Mutation(s): 0  Gene Names: FGO82_05925, SAMEA1711581_00005
UniProt
Find proteins for A0A4U9C0Y2 (Streptococcus pyogenes) Explore A0A4U9C0Y2  Go to UniProtKB:  A0A4U9C0Y2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9/Csn1	B [auth C]	1,368	Streptococcus pyogenes serotype M1	Mutation(s): 0  Gene Names: cas9, csn1, SPy_1046 EC: 3.1
UniProt
Find proteins for Q99ZW2 (Streptococcus pyogenes serotype M1) Explore Q99ZW2  Go to UniProtKB:  Q99ZW2

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (98-MER)	C [auth D]	92	Streptococcus pyogenes

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.68 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20_4459:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-01-21 
Deposition Author(s): Yu, L., Zhu, Y., Lu, Z., Huang, Z.

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

Revision History  

• Version 1.0: 2026-01-21
  Type: Initial release
  
• Version 1.1: 2026-08-05
  Changes: Data collection, Database references