2BJ6 | pdb_00002bj6

Crystal Structure of a decameric HNA-RNA hybrid

• PDB DOI: https://doi.org/10.2210/pdb2BJ6/pdb
• NAKB: 2BJ6

• Classification: NUCLEIC ACID (HNA/RNA)
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2005-01-30 Released: 2005-03-09 
• Deposition Author(s): Maier, T., Przylas, I., Straeter, N., Herdewijn, P., Saenger, W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.254 (Depositor) 
• R-Value Work: 
  0.217 (Depositor) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Reinforced Hna Backbone Hydration in the Crystal Structure of a Decameric Hna/RNA Hybrid

Maier, T., Przylas, I., Strater, N., Herdewijn, P., Saenger, W.

(2005) J Am Chem Soc 127: 2937

• PubMed: 15740130 
• DOI: https://doi.org/10.1021/ja045843v
• Primary Citation Related Structures: 
  2BJ6


• PubMed Abstract: 
  

  The crystal structure of a decameric HNA/RNA (HNA = 2',3'-dideoxy-1',5'-anhydro-d-arabinohexitol nucleic acid) hybrid with the RNA sequence 5'-GGCAUUACGG-3' is the first crystal structure of a hybrid duplex between a naturally occurring nucleic acid and a strand, which is fully modified to contain a six-membered ring instead of ribose. The presence of four duplex helices in the asymmetric unit allows for a detailed discussion of hydration, which revealed a tighter spinelike backbone hydration for the HNA- than for the RNA-strands. The reinforced backbone hydration is suggested to contribute significantly to the exceptional stability of HNA-containing duplexes and might be one of the causes for the evolutionary preference for ribose-derived nucleic acids.

---

Organizational Affiliation: 
• Institut für Chemie der Freien Universität Berlin, Takustrasse 6, 14195 Berlin, Germany.

Biological Assembly 1  

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

Biological Assembly 2  

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

Biological Assembly 3  

Biological assembly 3 assigned by authors and generated by PQS (software)

Biological Assembly 4  

Biological assembly 4 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 25.93 kDa 
• Atom Count: 1,876 
• Modeled Residue Count: 80 
• Deposited Residue Count: 80 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
SYNTHETIC HNA	A, B, C, D	10	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*CP*AP*UP*UP*AP*CP*GP*GP)-3'	E, F, G, H	10	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth B], J [auth C], K [auth E], L [auth G], M [auth G]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.254 (Depositor) 
• R-Value Work:  0.217 (Depositor) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.91	α = 90
b = 113.91	β = 90
c = 55.37	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-09 
Deposition Author(s): Maier, T., Przylas, I., Straeter, N., Herdewijn, P., Saenger, W.

Revision History  

• Version 1.0: 2005-03-09
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other