Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.27 kDa 
• Atom Count: 746 
• Modelled Residue Count: 34 
• Deposited Residue Count: 34 
• Unique nucleic acid chains: 1

1NBK

The structure of RNA aptamer for HIV Tat complexed with two argininamide molecules

• PDB DOI: 10.2210/pdb1NBK/pdb
• NDB: 1NBK

• Classification: RNA
• Mutation(s): No 


• Deposited: 2002-12-03 Released: 2003-12-03 
• Deposition Author(s): Matsugami, A., Kobayashi, S., Ouhashi, K., Uesugi, S., Yamamoto, R., Taira, K., Nishikawa, S., Kumar, P.K.R., Katahira, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Literature

Structural Basis of the Highly Efficient Trapping of the HIV Tat Protein by an RNA Aptamer

Matsugami, A., Kobayashi, S., Ouhashi, K., Uesugi, S., Yamamoto, R., Taira, K., Nishikawa, S., Kumar, P.K.R., Katahira, M.

(2003) Structure 11: 533-545

• PubMed: 12737819 
• DOI: 10.1016/s0969-2126(03)00069-8
• Primary Citation of Related Structures:  
  1NBK


• PubMed Abstract: 
  

An RNA aptamer containing two binding sites exhibits extremely high affinity to the HIV Tat protein. We have determined the structure of the aptamer complexed with two argininamide molecules. Two adjacent U:A:U base triples were formed, which widens the major groove to make space for the two argininamide molecules. The argininamide molecules bind to the G bases through hydrogen bonds. The binding is stabilized through stacking interactions. The structure of the aptamer complexed with a Tat-derived arginine-rich peptide was also characterized. It was suggested that the aptamer structure is similar for both complexes and that the aptamer interacts with two different arginine residues of the peptide simultaneously at the two binding sites, which could explain the high affinity to Tat.

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Organizational Affiliation: 

Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, 240-8501, Yokohama, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA aptamer	A	34	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GND	B [auth A], C [auth A]	2-AMINO-5-GUANIDINO-PENTANOIC ACID C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 1 
• OLDERADO: 1NBK Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-12-03 
• Released Date: 2003-12-03 
Deposition Author(s): Matsugami, A., Kobayashi, S., Ouhashi, K., Uesugi, S., Yamamoto, R., Taira, K., Nishikawa, S., Kumar, P.K.R., Katahira, M.

Revision History  

• Version 1.0: 2003-12-03
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Database references, Derived calculations