7ZKM

X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form beta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers.

Troisi, R.Riccardi, C.Perez de Carvasal, K.Smietana, M.Morvan, F.Del Vecchio, P.Montesarchio, D.Sica, F.

(2022) Mol Ther Nucleic Acids 30: 585-594

  • DOI: https://doi.org/10.1016/j.omtn.2022.11.007
  • Primary Citation of Related Structures:  
    7ZKL, 7ZKM, 7ZKN, 7ZKO

  • PubMed Abstract: 

    Despite their unquestionable properties, oligonucleotide aptamers display some drawbacks that continue to hinder their applications. Several strategies have been undertaken to overcome these weaknesses, using thrombin binding aptamers as proof-of-concept. In particular, the functionalization of a thrombin exosite I binding aptamer (TBA) with aromatic moieties, e.g., naphthalene dimides (N) and dialkoxynaphthalenes (D), attached at the 5' and 3' ends, respectively, proved to be highly promising. To obtain a molecular view of the effects of these modifications on aptamers, we performed a crystallographic analysis of one of these engineered oligonucleotides (TBA-NNp/DDp) in complex with thrombin. Surprisingly, three of the four examined crystallographic structures are ternary complexes in which thrombin binds a TBA-NNp/DDp molecule at exosite II as well as at exosite I, highlighting the ability of this aptamer, differently from unmodified TBA, to also recognize a localized region of exosite II. This novel ability is strictly related to the solvophobic behavior of the terminal modifications. Studies were also performed in solution to examine the properties of TBA-NNp/DDp in a crystal-free environment. The present results throw new light on the importance of appendages inducing a pseudo -cyclic charge-transfer structure in nucleic acid-based ligands to improve the interactions with proteins, thus considerably widening their potentialities.


  • Organizational Affiliation

    Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thrombin light chainA [auth L]36Homo sapiensMutation(s): 0 
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
GTEx:  ENSG00000180210 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Thrombin heavy chainB [auth H]259Homo sapiensMutation(s): 0 
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
GTEx:  ENSG00000180210 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P00734-1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
TBA-NNp/DDpC [auth A],
D [auth B]
15synthetic construct
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JL0 (Subject of Investigation/LOI)
Query on JL0

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B]
3-[13-methyl-5,7,12,14-tetrakis(oxidanylidene)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1(15),2,4(16),8,10-pentaen-6-yl]propyl 3-[5,7,12,14-tetrakis(oxidanylidene)-13-(3-oxidanylpropyl)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1,3,8(16),9,11(15)-pentaen-6-yl]propyl hydrogen phosphate
C43 H43 N4 O21 P3
FXOSPEYPRQTGKA-UHFFFAOYSA-N
JKR (Subject of Investigation/LOI)
Query on JKR

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B]
3-[5-[3-bis(oxidanyl)phosphanyloxypropoxy]naphthalen-1-yl]oxypropyl 3-(5-oxidanylnaphthalen-1-yl)oxypropyl hydrogen phosphate
C29 H34 O11 P2
ZWBSUQKVIPHNOV-UHFFFAOYSA-N
0G6
Query on 0G6

Download Ideal Coordinates CCD File 
F [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
K
Query on K

Download Ideal Coordinates CCD File 
J [auth A],
M [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA
Query on NA

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G [auth H]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.6α = 90
b = 76.6β = 90
c = 129.38γ = 120
Software Package:
Software NamePurpose
autoPROCdata processing
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2022-12-14
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Database references, Refinement description