9JG3 | pdb_00009jg3

Structure of Cas12p-TrxA-guide RNA-target DNA complex(33-bp dsDNA)

• PDB DOI: https://doi.org/10.2210/pdb9JG3/pdb
• EM Map EMD-61449: EMDB EMDataResource
• NAKB: 9JG3

• Classification: RNA BINDING PROTEIN/RNA/DNA
• Organism(s): unidentified, synthetic construct, Escherichia coli BL21(DE3)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-05 Released: 2025-09-10 
• Deposition Author(s): Wang, Z.P., Wang, Y.J., Ji, Q.J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Host thioredoxin is a CRISPR enhancer of phage-encoded miniature Cas12p nucleases

Wang, Z.P., Wang, Y.J., Ji, Q.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 196.27 kDa 
• Atom Count: 9,188 
• Modeled Residue Count: 858 
• Deposited Residue Count: 1,162 
• Unique protein chains: 2
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas12p	A	741	unidentified	Mutation(s): 0
UniProt
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12306  Go to UniProtKB:  Q12306

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin	E	109	Escherichia coli BL21(DE3)	Mutation(s): 0
UniProt
Find proteins for P0AA25 (Escherichia coli (strain K12)) Explore P0AA25  Go to UniProtKB:  P0AA25

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (246-MER)	B	246	unidentified

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (33-MER)	C	33	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (33-MER)	D	33	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286:
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Wang, Z.P., Wang, Y.J., Ji, Q.J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22277078

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release