7BPF

Structure of L-threoninol nucleic acid - RNA complex

• PDB DOI: https://doi.org/10.2210/pdb7BPF/pdb
• NAKB: 7BPF

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


• Deposited: 2020-03-22 Released: 2020-11-25 
• Deposition Author(s): Kamiya, Y., Satoh, T., Kodama, A., Suzuki, T., Uchiyama, S., Kato, K., Asanuma, H.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.288 
• R-Value Work: 0.269 
• R-Value Observed: 0.270 

Literature

Intrastrand backbone-nucleobase interactions stabilize unwound right-handed helical structures of heteroduplexes of L-aTNA/RNA and SNA/RNA

Kamiya, Y., Satoh, T., Kodama, A., Suzuki, T., Murayama, K., Kashida, H., Uchiyama, S., Kato, K., Asanuma, H.

(2020) Commun Chem 

• DOI: https://doi.org/10.1038/s42004-020-00400-2

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.76 kDa 
• Atom Count: 671 
• Modelled Residue Count: 30 
• Deposited Residue Count: 30 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')	A, B	7	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
L-aTNA (3'-(*GP*CP*AP*GP*CP*AP*GP*C)-1')	C, D	8	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.288 
• R-Value Work: 0.269 
• R-Value Observed: 0.270 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.996	α = 90
b = 33.344	β = 115.64
c = 54.055	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-11-25 
Deposition Author(s): Kamiya, Y., Satoh, T., Kodama, A., Suzuki, T., Uchiyama, S., Kato, K., Asanuma, H.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History  

• Version 1.0: 2020-11-25
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references, Derived calculations