3QLP

X-ray structure of the complex between human alpha thrombin and a modified thrombin binding aptamer (mTBA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Thrombin-aptamer recognition: a revealed ambiguity.

Russo Krauss, I.Merlino, A.Giancola, C.Randazzo, A.Mazzarella, L.Sica, F.

(2011) Nucleic Acids Res 39: 7858-7867

  • DOI: 10.1093/nar/gkr522
  • Primary Citation of Related Structures:  
    3QLP

  • PubMed Abstract: 
  • Aptamers are structured oligonucleotides that recognize molecular targets and can function as direct protein inhibitors. The best-known example is the thrombin-binding aptamer, TBA, a single-stranded 15-mer DNA that inhibits the activity of thrombin, ...

    Aptamers are structured oligonucleotides that recognize molecular targets and can function as direct protein inhibitors. The best-known example is the thrombin-binding aptamer, TBA, a single-stranded 15-mer DNA that inhibits the activity of thrombin, the key enzyme of coagulation cascade. TBA folds as a G-quadruplex structure, as proved by its NMR structure. The X-ray structure of the complex between TBA and human α-thrombin was solved at 2.9-Å resolution, but did not provide details of the aptamer conformation and the interactions with the protein molecule. TBA is rapidly processed by nucleases. To improve the properties of TBA, a number of modified analogs have been produced. In particular, a modified TBA containing a 5'-5' polarity inversion site, mTBA, has higher stability and higher affinity toward thrombin with respect to TBA, although it has a lower inhibitory activity. We present the crystal structure of the thrombin-mTBA complex at 2.15-Å resolution; the resulting model eventually provides a clear picture of thrombin-aptamers interaction, and also highlights the structural bases of the different properties of TBA and mTBA. Our findings open the way for a rational design of modified aptamers with improved potency as anticoagulant drugs.


    Organizational Affiliation

    Università di Napoli Federico II, Via Cintia, Napoli, Italia.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin heavy chainH259Homo 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
Thrombin light chainL36Homo 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
    modified thrombin binding DNA aptamerD15N/A
    Small Molecules
    Ligands 4 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
    2-acetamido-2-deoxy-beta-D-glucopyranose
    C8 H15 N O6
    OVRNDRQMDRJTHS-FMDGEEDCSA-N
     Ligand Interaction
    K
    Query on K

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

    Download CCD File 
    H
    SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Biologically Interesting Molecules (External Reference) 1 Unique
    Entity ID: 4
    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: 2.14 Å
    • R-Value Free: 0.237 
    • R-Value Work: 0.183 
    • R-Value Observed: 0.186 
    • Space Group: I 2 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 68.208α = 90
    b = 110.574β = 90
    c = 120.916γ = 90
    Software Package:
    Software NamePurpose
    CrystalCleardata collection
    AMoREphasing
    CNSrefinement
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2011-10-19
      Type: Initial release
    • Version 1.1: 2013-02-27
      Changes: Other
    • Version 1.2: 2020-07-29
      Type: Remediation
      Reason: Carbohydrate remediation
      Changes: Advisory, Data collection, Derived calculations, Structure summary