4DII

X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of potassium ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity.

Russo Krauss, I.Merlino, A.Randazzo, A.Novellino, E.Mazzarella, L.Sica, F.

(2012) Nucleic Acids Res 40: 8119-8128

  • DOI: 10.1093/nar/gks512
  • Primary Citation of Related Structures:  
    4DII, 4DIH

  • PubMed Abstract: 
  • The G-quadruplex architecture is a peculiar structure adopted by guanine-rich oligonucleotidic sequences, and, in particular, by several aptamers, including the thrombin-binding aptamer (TBA) that has the highest inhibitory activity against human α-throm ...

    The G-quadruplex architecture is a peculiar structure adopted by guanine-rich oligonucleotidic sequences, and, in particular, by several aptamers, including the thrombin-binding aptamer (TBA) that has the highest inhibitory activity against human α-thrombin. A crucial role in determining structure, stability and biological properties of G-quadruplexes is played by ions. In the case of TBA, K(+) ions cause an enhancement of the aptamer clotting inhibitory activity. A detailed picture of the interactions of TBA with the protein and with the ions is still lacking, despite the importance of this aptamer in biomedical field for detection and inhibition of α-thrombin. Here, we fill this gap by presenting a high-resolution crystallographic structural characterization of the thrombin-TBA complex formed in the presence of Na(+) or K(+) and a circular dichroism study of the structural stability of the aptamer both free and complexed with α-thrombin, in the presence of the two ionic species. The results indicate that the different effects exerted by Na(+) and K(+) on the inhibitory activity of TBA are related to a subtle perturbation of a few key interactions at the protein-aptamer interface. The present data, in combination with those previously obtained on the complex between α-thrombin and a modified aptamer, may allow the design of new TBA variants with a pharmacological performance enhancement.


    Related Citations: 
    • Thrombin-aptamer recognition: a revealed ambiguity.
      Russo Krauss, I., Merlino, A., Giancola, C., Randazzo, A., Mazzarella, L., Sica, F.
      (2011) Nucleic Acids Res 39: 7858
    • The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer.
      Padmanabhan, K., Padmanabhan, K.P., Ferrara, J.D., Sadler, J.E., Tulinsky, A.
      (1993) J Biol Chem 268: 17651
    • An ambiguous structure of a DNA 15-mer thrombin complex.
      Padmanabhan, K., Tulinsky, A.
      (1996) Acta Crystallogr D Biol Crystallogr 52: 272

    Organizational Affiliation

    Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Via Cintia, I-80126 Napoli, Italia.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Prothrombin L36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Prothrombin H259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    Thrombin binding aptamerD15synthetic construct
    Small Molecules
    Ligands 6 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    0G6
    Query on 0G6

    Download Ideal Coordinates CCD File 
    H
    D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
    C21 H34 Cl N6 O3
    DVFLYEYCMMLBTQ-VSZNYVQBSA-O
     Ligand Interaction
    NAG
    Query on NAG

    Download Ideal Coordinates CCD File 
    H
    2-acetamido-2-deoxy-beta-D-glucopyranose
    C8 H15 N O6
    OVRNDRQMDRJTHS-FMDGEEDCSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    H, L
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    K
    Query on K

    Download Ideal Coordinates CCD File 
    D
    POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    CL
    Query on CL

    Download Ideal Coordinates CCD File 
    H
    CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M
     Ligand Interaction
    NA
    Query on NA

    Download Ideal Coordinates CCD File 
    H
    SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Biologically Interesting Molecules (External Reference) 1 Unique
    Entity ID: 5
    IDChainsNameType/Class2D Diagram3D Interactions
    PRD_000020 (0G6)
    Query on PRD_000020
    HD-Phe-Pro-Arg-CH2ClPeptide-like /  Inhibitor

    --

    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.05 Å
    • R-Value Free: 0.226 
    • R-Value Work: 0.174 
    • R-Value Observed: 0.195 
    • Space Group: P 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 43.369α = 68.97
    b = 45.299β = 86.11
    c = 51.519γ = 69.66
    Software Package:
    Software NamePurpose
    CrystalCleardata collection
    PHASESphasing
    CNSrefinement
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2012-07-18
      Type: Initial release
    • Version 1.1: 2012-09-26
      Changes: Database references
    • Version 1.2: 2013-02-27
      Changes: Other
    • Version 1.3: 2020-07-29
      Type: Remediation
      Reason: Carbohydrate remediation
      Changes: Data collection, Derived calculations, Structure summary