4U6K | pdb_00004u6k

Crystal structure of DNA/RNA duplex containing 2'-4'-BNA-NC

• PDB DOI: https://doi.org/10.2210/pdb4U6K/pdb
• NAKB: 4U6K

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


• Deposited: 2014-07-29 Released: 2015-08-19 
• Deposition Author(s): Kondo, J., Nomura, Y., Kitahara, Y., Obika, S., Torigoe, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.196 (DCC) 

Literature

The crystal structure of a 2',4'-BNA(NC)[N-Me]-modified antisense gapmer in complex with the target RNA.

Kondo, J., Nomura, Y., Kitahara, Y., Obika, S., Torigoe, H.

(2016) Chem Commun (Camb) 52: 2354-2357

• PubMed: 26731288 
• DOI: https://doi.org/10.1039/c5cc08300a
• Primary Citation Related Structures: 
  4U6K, 4U6L, 4U6M


• PubMed Abstract: 
  

  It has been confirmed by our previous studies that a 2',4'-BNA(NC)[N-Me]-modified antisense gapmer displays high affinity and selectivity to the target RNA strand, promising mRNA inhibitory activity and excellent nuclease resistance. Herein, we have obtained a crystal structure that provides insights into these excellent antisense properties.

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Organizational Affiliation: 
• Department of Materials and Life Sciences, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo, Japan. [e-mail].
Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, 162-8601 Tokyo, Japan. [e-mail] and Division of Medical Devices, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, 158-8501 Tokyo, Japan.
Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, 565-0871 Osaka, Japan. [e-mail].
Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, 162-8601 Tokyo, Japan. [e-mail].

Biological Assembly 1  

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

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 12.23 kDa 
• Atom Count: 1,156 
• Modeled Residue Count: 36 
• Deposited Residue Count: 36 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')	A, C	9	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*(NCU)P*(NTT)P*CP*TP*TP*CP*TP*(NTT)P*(NCU))-3')	B, D	9	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	E [auth A], F [auth A], G [auth C]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.196 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.92	α = 90
b = 58.96	β = 90
c = 102.44	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data reduction
PHENIX	phasing
CNS	refinement
PDB_EXTRACT	data extraction
SOLVE	model building
d*TREK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-19 
Deposition Author(s): Kondo, J., Nomura, Y., Kitahara, Y., Obika, S., Torigoe, H.

Revision History  

• Version 1.0: 2015-08-19
  Type: Initial release
  
• Version 1.1: 2020-01-29
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.2: 2022-07-06
  Changes: Database references
• Version 1.3: 2024-06-26
  Changes: Data collection