9EBU | pdb_00009ebu

Wild-type EsCas13d binary complex

• PDB DOI: https://doi.org/10.2210/pdb9EBU/pdb
• NAKB: 9EBU
• EM Map EMD-47892: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): [Eubacterium] siraeum DSM 15702
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-13 Released: 2025-11-19 
• Deposition Author(s): Chou, C.W., Finkelstein, I.J.
• Funding Organization(s): Welch Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.06 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural Basis for Target Discrimination and Activation by Cas13d

Chou, C.W., Finkelstein, I.J.

To be published.

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: 127.59 kDa 
• Atom Count: 8,097 
• Modeled Residue Count: 909 
• Deposited Residue Count: 1,006 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EsCas13d	A	954	[Eubacterium] siraeum DSM 15702	Mutation(s): 0  Gene Names: EUBSIR_02687
UniProt
Find proteins for B0MS50 ([Eubacterium] siraeum DSM 15702) Explore B0MS50  Go to UniProtKB:  B0MS50

Entity ID: 2
Molecule	Chains	Length	Organism	Image
crRNA	B	52	[Eubacterium] siraeum DSM 15702

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.06 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Chou, C.W., Finkelstein, I.J.

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Funding Organization	Location	Grant Number
Welch Foundation	United States	F-1808

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release