9LZU | pdb_00009lzu

RfxCas13d-crRNA-target RNA ternary complex

• PDB DOI: https://doi.org/10.2210/pdb9LZU/pdb
• EM Map EMD-63531: EMDB EMDataResource
• NAKB: 9LZU

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Ruminococcus sp. XPD3002, Cloning vector pgRNA-ccdB-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-02-22 Released: 2025-10-08 
• Deposition Author(s): Yang, Q.X., Sun, Y.F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

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

Literature

RfxCas13d-crRNA-target RNA ternary complex

Yang, Q.X., Sun, Y.F.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 132.38 kDa 
• Atom Count: 8,364 
• Modeled Residue Count: 918 
• Deposited Residue Count: 1,031 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RfxCas13d	A	966	Ruminococcus sp. XPD3002	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (51-MER)	B [auth C]	51	Cloning vector pgRNA-ccdB-1

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*CP*UP*GP*UP*GP*GP*GP*AP*CP*GP*AP*GP*UP*C)-3')	C [auth B]	14	Cloning vector pgRNA-ccdB-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	D [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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	1.20.1_4487

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Yang, Q.X., Sun, Y.F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	92469108
National Natural Science Foundation of China (NSFC)	China	31970146

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release