6TXR

Structural insights into cubane-modified aptamer recognition of a malaria biomarker


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Evolution of abiotic cubane chemistries in a nucleic acid aptamer allows selective recognition of a malaria biomarker.

Cheung, Y.W.Rothlisberger, P.Mechaly, A.E.Weber, P.Levi-Acobas, F.Lo, Y.Wong, A.W.C.Kinghorn, A.B.Haouz, A.Savage, G.P.Hollenstein, M.Tanner, J.A.

(2020) Proc Natl Acad Sci U S A 117: 16790-16798

  • DOI: https://doi.org/10.1073/pnas.2003267117
  • Primary Citation of Related Structures:  
    6TXR

  • PubMed Abstract: 

    Nucleic acid aptamers selected through systematic evolution of ligands by exponential enrichment (SELEX) fold into exquisite globular structures in complex with protein targets with diverse translational applications. Varying the chemistry of nucleotides allows evolution of nonnatural nucleic acids, but the extent to which exotic chemistries can be integrated into a SELEX selection to evolve nonnatural macromolecular binding interfaces is unclear. Here, we report the identification of a cubane-modified aptamer (cubamer) against the malaria biomarker Plasmodium vivax lactate dehydrogenase (PvLDH). The crystal structure of the complex reveals an unprecedented binding mechanism involving a multicubane cluster within a hydrophobic pocket. The binding interaction is further stabilized through hydrogen bonding via cubyl hydrogens, previously unobserved in macromolecular binding interfaces. This binding mechanism allows discriminatory recognition of P. vivax over Plasmodium falciparum lactate dehydrogenase, thereby distinguishing these highly conserved malaria biomarkers for diagnostic applications. Together, our data demonstrate that SELEX can be used to evolve exotic nucleic acids bearing chemical functional groups which enable remarkable binding mechanisms which have never been observed in biology. Extending to other exotic chemistries will open a myriad of possibilities for functional nucleic acids.


  • Organizational Affiliation

    School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-lactate dehydrogenase
A, B, C, D
316Plasmodium vivaxMutation(s): 0 
Gene Names: LDHldhPVC01_120033300PVP01_1229700PVT01_120033900
EC: 1.1.1.27
UniProt
Find proteins for Q4PRK9 (Plasmodium vivax)
Explore Q4PRK9 
Go to UniProtKB:  Q4PRK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4PRK9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DG
Query on DG

Download Ideal Coordinates CCD File 
AA [auth A]
AC [auth D]
BA [auth A]
DB [auth C]
FB [auth C]
AA [auth A],
AC [auth D],
BA [auth A],
DB [auth C],
FB [auth C],
G [auth A],
GB [auth C],
H [auth A],
HB [auth C],
J [auth A],
LB [auth C],
MA [auth B],
MB [auth C],
OA [auth B],
S [auth A],
SA [auth C],
TA [auth C],
TB [auth D],
U [auth A],
V [auth A],
W [auth A],
YB [auth D]
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
LTFMZDNNPPEQNG-KVQBGUIXSA-N
DA
Query on DA

Download Ideal Coordinates CCD File 
AB [auth C]
CA [auth A]
EB [auth C]
FA [auth B]
HA [auth B]
AB [auth C],
CA [auth A],
EB [auth C],
FA [auth B],
HA [auth B],
JB [auth C],
K [auth A],
NA [auth B],
NB [auth C],
P [auth A],
QB [auth D],
SB [auth D],
T [auth A],
VA [auth C],
Y [auth A],
ZB [auth D]
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O6 P
KHWCHTKSEGGWEX-RRKCRQDMSA-N
DU
Query on DU

Download Ideal Coordinates CCD File 
BC [auth D]
GA [auth B]
I [auth A]
LA [auth B]
O [auth A]
BC [auth D],
GA [auth B],
I [auth A],
LA [auth B],
O [auth A],
PA [auth B],
RB [auth D],
UA [auth C],
XB [auth D],
ZA [auth C]
2'-DEOXYURIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
DC
Query on DC

Download Ideal Coordinates CCD File 
BB [auth C]
CB [auth C]
IA [auth B]
IB [auth C]
JA [auth B]
BB [auth C],
CB [auth C],
IA [auth B],
IB [auth C],
JA [auth B],
KA [auth B],
KB [auth C],
L [auth A],
M [auth A],
N [auth A],
Q [auth A],
R [auth A],
UB [auth D],
VB [auth D],
WA [auth C],
WB [auth D],
X [auth A],
XA [auth C],
YA [auth C],
Z [auth A]
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O7 P
NCMVOABPESMRCP-SHYZEUOFSA-N
O0Q (Subject of Investigation/LOI)
Query on O0Q

Download Ideal Coordinates CCD File 
DA [auth B]
E [auth A]
EA [auth B]
F [auth A]
OB [auth D]
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
OB [auth D],
PB [auth D],
QA [auth C],
RA [auth C]
~{N}-[2-(1,2,3-triazol-1-yl)ethyl]cubane-1-carboxamide
C13 H14 N4 O
OEUPRBXQNJLJSP-NFVYEKIASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.72α = 90
b = 80.72β = 90
c = 504.77γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Pasteur InstituteFrance--
Shirley Boyde FoundationHong Kong--

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Advisory, Data collection, Database references, Refinement description