7BPG

Structure of serinol nucleic acid - RNA complex

• PDB DOI: https://doi.org/10.2210/pdb7BPG/pdb
• NAKB: 7BPG

• 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: 1.70 Å
• R-Value Free: 0.271 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 

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.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.34 kDa 
• Atom Count: 1,395 
• Modelled Residue Count: 63 
• Deposited Residue Count: 64 
• 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 [auth C], C [auth E], D [auth G]	8	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
SNA (S-(F7R)(F7X)(F7O)(F7R)(F7X)(F7O)(F7R)(F7U)-R)	E [auth B], F [auth D], G [auth F], H	8	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.271 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.363	α = 90
b = 46.918	β = 114.54
c = 47.54	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