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, the key enzyme of coagulation cascade ...

    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 chainA [auth H]259Homo 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 chainB [auth L]36Homo 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 nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    modified thrombin binding DNA aptamerC [auth D]15N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    0G6
    Query on 0G6

    Download Ideal Coordinates CCD File 
    D [auth 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 
    E [auth H]2-acetamido-2-deoxy-beta-D-glucopyranose
    C8 H15 N O6
    OVRNDRQMDRJTHS-FMDGEEDCSA-N
     Ligand Interaction
    K
    Query on K

    Download Ideal Coordinates CCD File 
    G [auth D]POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    NA
    Query on NA

    Download Ideal Coordinates CCD File 
    F [auth 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
    D [auth H]D-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  (Full details and data files)

    • 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