1NTA | pdb_00001nta

2.9 A crystal structure of Streptomycin RNA-aptamer

• PDB DOI: https://doi.org/10.2210/pdb1NTA/pdb
• NAKB: 1NTA

• Classification: RNA
• Mutation(s): No 


• Deposited: 2003-01-29 Released: 2003-05-13 
• Deposition Author(s): Tereshko, V., Skripkin, E., Patel, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.282 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Encapsulating Streptomycin within a small 40-mer RNA

Tereshko, V., Skripkin, E., Patel, D.J.

(2003) Chem Biol 10: 175-187

• PubMed: 12618190 
• DOI: https://doi.org/10.1016/s1074-5521(03)00024-3
• Primary Citation Related Structures: 
  1NTA, 1NTB


• PubMed Abstract: 
  

  We describe a 2.9 A X-ray structure of a complex between the aminocyclitol antibiotic streptomycin and an in vitro selected RNA aptamer, solved using the anomalous diffraction properties of Ba cations. The RNA aptamer, which contains two asymmetric internal loops, adopts a distinct cation-stabilized fold involving a series of S-shaped backbone turns anchored by canonical and noncanonical pairs and triples. The streptomycin streptose ring is encapsulated by stacked arrays of bases from both loops at the elbow of the L-shaped RNA architecture. Specificity is defined by direct hydrogen bonds between all streptose functional groups and base edges that line the inner walls of the cylindrical binding pocket. By contrast, the majority of intermolecular interactions involve contacts to backbone phosphates in the published structure of streptomycin bound to the 16S rRNA.

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Organizational Affiliation: 
• Cellular Biochemistry & Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.79 kDa 
• Atom Count: 887 
• Modeled Residue Count: 40 
• Deposited Residue Count: 40 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*AP*UP*CP*GP*CP*AP*UP*UP*UP*GP*GP*AP*CP*UP*UP*CP*UP*GP*CP*C)-3'	A	22	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*CP*GP*GP*CP*AP*CP*CP*AP*CP*GP*GP*UP*CP*GP*GP*AP*UP*C)-3'	B	18	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SRY	F [auth A]	STREPTOMYCIN C21 H39 N7 O12 UCSJYZPVAKXKNQ-HZYVHMACSA-N
BA	C [auth A], G [auth B], H [auth B]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N
NA	D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.282 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.097	α = 90
b = 83.097	β = 90
c = 49.472	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-05-13 
Deposition Author(s): Tereshko, V., Skripkin, E., Patel, D.J.

Revision History  

• Version 1.0: 2003-05-13
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-05-10
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations