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 1.2 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
  • Structures With Same Primary Citation

  • 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-t ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prothrombin
L
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Prothrombin
H
259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
Thrombin binding aptamerD15synthetic construct
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0G6
Query on 0G6

Download 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 CCD File 
H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ZN
Query on ZN

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

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

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

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

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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