4DIH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.167 

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
  • Primary Citation of Related Structures:  
  • Also Cited By: 4I7Y

  • 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.,Sect.D 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 Gene View: F2
Go to UniProtKB:  P00734
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 Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 3
MoleculeChainsLengthOrganism
Thrombin binding aptamerD15synthetic construct
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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Download CCD File 
D, H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
0G6
Query on 0G6

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

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H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NAG
Query on NAG

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H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-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: 1.8 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.167 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 43.018α = 65.22
b = 44.716β = 85.33
c = 52.689γ = 69.97
Software Package:
Software NamePurpose
CNSphasing
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2012-09-26
    Type: Database references
  • Version 1.2: 2013-02-27
    Type: Other