1NBK

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


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

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This is version 1.3 of the entry. See complete history


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

  • 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 ...

    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.


    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
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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA aptamerA 34N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GND
Query on GND

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
2-AMINO-5-GUANIDINO-PENTANOIC ACID
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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