Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.61 kDa 
• Atom Count: 2840 
• Residue Count: 291 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

4DIH

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

• DOI: 10.2210/pdb4DIH/pdb
• NDB: NA1566

• Classification: HYDROLASE/HYDROLASE INHIBITOR/DNA
• Organism(s): Homo sapiens, synthetic construct
• Mutation(s): No 


• Deposited: 2012-01-31 Released: 2012-07-18 
• Deposition Author(s): Russo Krauss, I., Merlino, A., Mazzarella, L., Sica, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.213 
• R-Value Work: 0.167 
• R-Value Observed: 0.186 

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

• PubMed: 22669903 
• DOI: 10.1093/nar/gks512
• Primary Citation of Related Structures:  
  4DII, 4DIH


• 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-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.

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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

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Organizational Affiliation: 

Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Via Cintia, I-80126 Napoli, Italia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	L	36	Homo sapiens	Mutation(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 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	H	259	Homo sapiens	Mutation(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 GTEx:  ENSG00000180210

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Thrombin binding aptamer	D	15	synthetic construct

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0G6	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
NAG	H	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	H, L	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	H	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D, H	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000020 (0G6)	H	D-Phe-Pro-Arg-CH2Cl	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.213 
• R-Value Work: 0.167 
• R-Value Observed: 0.186 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.018	α = 65.22
b = 44.716	β = 85.33
c = 52.689	γ = 69.97

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-31 
• Released Date: 2012-07-18 
Deposition Author(s): Russo Krauss, I., Merlino, A., Mazzarella, L., Sica, F.

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
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary