9KGH | pdb_00009kgh

Cryo-EM structure of circular intron of thymidylate synthase (td) gene of bacteriophage T4

• PDB DOI: https://doi.org/10.2210/pdb9KGH/pdb
• NAKB: 9KGH
• EM Map EMD-62319: EMDB EMDataResource

• Classification: RNA
• Organism(s): Escherichia phage T4
• Expression System: in vitro transcription vector pT7-Fluc(deltai)
• Mutation(s): No 


• Deposited: 2024-11-08 Released: 2025-11-12 
• Deposition Author(s): An, L., Li, S., Zhang, K.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanistic Insights into Cyclization of the T4 td Group I Intron

An, L., Li, S., Zhang, K.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 85.02 kDa 
• Atom Count: 5,625 
• Modeled Residue Count: 264 
• Deposited Residue Count: 264 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (264-MER)	A [auth U]	264	Escherichia phage T4

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	4.5.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): An, L., Li, S., Zhang, K.

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Funding Organization	Location	Grant Number
Other government		--

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release