7A3Y

RNA duplex with a cytosine bulge in complex with berberine

• PDB DOI: https://doi.org/10.2210/pdb7A3Y/pdb
• NAKB: 7A3Y
• BMRB: 34553

• Classification: RNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2020-08-19 Released: 2021-03-10 
• Deposition Author(s): Podbevsek, P., Plavec, J.
• Funding Organization(s): Slovenian Research Agency

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Interaction between berberine and RNA for the exploration of phytochemicals role

Podbevsek, P., Plavec, J.

(2021) Nucleic Acids Res 

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 8.3 kDa 
• Atom Count: 551 
• Modelled Residue Count: 25 
• Deposited Residue Count: 25 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA-A chain A	A	13	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA-A chain B	B	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BER (Subject of Investigation/LOI)	C [auth A]	BERBERINE C20 H18 N O4 YBHILYKTIRIUTE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-10 
Deposition Author(s): Podbevsek, P., Plavec, J.

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Funding Organization	Location	Grant Number
Slovenian Research Agency	Slovenia	P1-0242

Revision History  

• Version 1.0: 2021-03-10
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Database references, Other