GZNL's Respiratory Data Centre, GZNL-RDC

Ribocentre-aptamer

A database of RNA aptamers

Example: RNA aptamer   SELEX   ATP-aptamer   Structure  


Aptamer applications

Structures

This page provides a summary of the methods used for structure determination and phasing in RNA aptamer structure research. Additionally, we provide a comprehensive list of all the structured RNA aptamer included in this collection, along with their respective Protein Data Bank (PDB) entries.


Statistical information

A statistical analysis has been conducted on the structural determination and phase elucidation of RNA aptamers. Upper left figure: A statistical summary of structural elucidation methods for RNA aptamers, including X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM). Upper right figure: A statistical summary of solutions to phase problems generated by X-ray structural elucidation, such as Molecular Replacement (MR). Lower left figure: A statistical summary of phase problem solutions for aptamers targeting small molecules. Lower right figure: A statistical summary of phase problem solutions for aptamers targeting proteins and nucleic acids.

drawing drawing


Detailed information

This section displays




Small molecules

Category Name Ligand Structure Determination NDB Phase Determination Resolution(Å) Year
Biologics & Signaling Molecules FMN aptamer FMN NMR 1FMN NA NA 1996
Amino Acids & Peptides Arginine aptamer Arginine NMR 1KOC NA NA 1996
Amino Acids & Peptides Citrulline aptamer Citrulline NMR 1KOD NA NA 1996
Biologics & Signaling Molecules Vitamin B12-aptamer Vitamin B12 X-ray 1ET4
1DDY		 molecular replacement(MR),
Co(MAD)		 2.3
>3.0		 2000a
2000b
Biologics & Signaling Molecules Biotin aptamer Biotin X-ray 1F27 Se (MAD) 1.3 2000
Biologics & Signaling Molecules 5HTP-aptamer 5-HT X-ray 5KPY Ir (SIRAS) 2.0 2017
Biologics & Signaling Molecules Riboflavin aptamer FMN NMR 7RWR NA NA 2022
Pharmaceuticals Theophylline-aptamer TAL3
theophylline
apo
TAL2
TAL1
TAL4		 X-ray 8D2A
8D28
8D29
8D2B
8D5L
8D5O		 molecular replacement(MR) 2.17
1.42
1.81
1.44
1.64
2.7		 2022
Fluorophores MG aptamer tetramethylrosamine(TMR)
malachite green		 X-ray 1F1T Br (MAD) 2.8 2000
NMR 1Q8N NA NA 2004
Fluorophores Spinach aptamer DFHBI-1T
DFHBI
DFHBI
trifluoroethyl, Fab
1TU, Fab
bromo-ligand analog, Fab		 X-ray 4TS0
4TS2
5OB3
4Q9R
4KZD
4Q9Q		 Ba (SAD),
molecular replacement(MR)		 2.8
2.88
2.0
3.12
2.19
2.45		 2014a
2014b
2017
Fluorophores GTP aptamer GTP NMR 5LWJ
2AU4		 NA NA 2006
2017
Fluorophores Corn aptamer DFHO
DFHO
ThT
ThT
TO
apo		 X-ray 5BJP
5BJO
6E81
6E82
6E84
6E80		 Ir (SAD),
molecular replacement(MR)		 2.51
2.35
2.721
3.1
2.9
2.9		 2017
2019
Fluorophores Mango aptamer(TO1-biotin) TO1-Biotin
TO1-Biotin
TO3-Biotin
TO1-Biotin
TO1-Biotin
TO1-Biotin		 X-ray 5V3F
6C63
6C64
6C65
6V9B
6V9D		 Ir (SAD),
molecular replacement(MR)		 1.7
2.9
3.0
2.8
2.4
2.8		 2017
2018
2020
Fluorophores DIR2s-apt aptamer oxazole thiazole blue (OTB) X-ray 6DB9
6DB8		 molecular replacement(MR) 2.025 2018
Fluorophores Mango-III aptamer(YO3) TO1-Biotin
TO1-Biotin
TO1-Biotin
TO1-Biotin
YO3-Biotin
DFHBI-1T		 X-ray 6E8S
6E8T
6E8U
6PQ7
6UP0
7L0Z		 Ir(SAD),
molecular replacement(MR)		 2.35
2.9
1.55
3.0
2.8
2.1		 2019a
2019b
2021
Fluorophores TMR aptamer tetramethylrhodamine NMR 6GZR
6GZK		 NA NA 2020
Fluorophores Chili aptamer DMHBI+
DMHBO+
DMHBO+
DMHBO+		 X-ray 7OAW
7OA3
7OAV
7OAX		 molecular replacement(MR),
Ir (SAD)		 2.95
2.8
2.99
2.24		 2021
Fluorophores Pepper aptamer HBC
HBC
HBC
HBC
HBC485
HBC497
HBC508
HBC514
HBC525
HBC620
HBC599 and Fab BL3-6
HBC and Fab BL3-6		 X-ray 7EOH
7EOG
7EOI
7EOJ
7EOK
7EOL
7EOM
7EON
7EOO
7EOP
7U0Y
7SZU		 Ir (SAD),
molecular replacement(MR)		 1.64
1.5
1.92
1.77
2.7
2.31
2.7
2.3
2.23
1.8
2.66
2.24		 2021
2022
Fluorophores Squash aptamer DFHBI-1T X-ray 7KVT
7KVU
7KVV		 Ir (SAD),
molecular replacement(MR)		 2.73
2.68
2.85		 2022
Fluorophores Beetroot aptamer DFAME
ThT
DFHO
DFHO		 X-ray 8EYU
8EYW
8F0N
8EYV		 molecular replacement(MR) 1.95
2.1
2.85
2.55		 2023
Nucleosides & Nucleotides AMP aptamer AMP NMR 1AM0
1RAW		 NA NA 1996a
1996b
Nucleosides & Nucleotides ATP aptamer AMPNAapo EM 6WLJ
6WLK		 NA 9.6 2020
Pharmaceuticals Tobramycin-RNA aptamer Aminoglycoside
tobramycin		 NMR 1TOB
2TOB		 NA NA 1997
1998
Pharmaceuticals Theophylline-aptamer theophylline NMR 1EHT
1O15		 NA NA 1997
2003
Pharmaceuticals NeomycinB RNA aptamer neomycin B NMR 1NEM NA NA 1999
Pharmaceuticals Streptomycin-RNA Aptamer Streptomycin X-ray 1NTA
1NTB		 Ba (MAD) 2.9 2003
Pharmaceuticals Tetracycline aptamer tetracycline X-ray 3EGZ Se (MAD) 2.2 2008

Proteins

Category Name Ligand Structure Determination NDB Phase Determination Resolution(Å) Year
Bacteria Hfq aptamer YmaH (Hfq) X-ray 3HSB
3AHU		 molecular replacement(MR) 2.2 2012
Bacteria Ribosomal protein S8-aptamer ribosomal protein S8 X-ray 4PDB molecular replacement(MR) 2.6 2014a
NMR 2LUN NA NA 2014b
Bacteria TetR aptamer transcription repressor TetR X-ray 6SY4
6SY6		 molecular replacement(MR) 2.69
2.9		 2020
Mammalian GlnRs aptamer GlnRS
Gln		 X-ray 1EXD molecular replacement(MR) 2.7 2000
Mammalian NF-kappaB aptamer NF-kappaB X-ray 1OOA molecular replacement(MR) and single isomorphous replacement (SIR) methods 2.45 2003
NMR 2JWV NA NA 2008
Mammalian (eIF4A)-aptamer initiation factor 4A (eIF4A) NMR 1XWP
1XWU		 NA NA 2005
Mammalian FC RNA aptamer RNA polymerase (Pol) II X-ray 2B63 Br (SAD) 3.8 2005
Mammalian Thrombin aptamer human thrombin X-ray 3DD2 molecular replacement(MR) 1.9 2008
Mammalian IgG aptamer human IgG X-ray 3AGV molecular replacement(MR) 2.15 2010
Mammalian GRK2 aptamer G protein-coupled receptor kinase 2 (GRK2) X-ray 3UZT
3UZS		 molecular replacement(MR) 3.51 2012
Mammalian lysozyme aptamer lysozyme X-ray 4M6D
4M4O		 molecular replacement(MR) 2.68
2.0		 2013
Mammalian NOX-E36 L-aptamer L-CLL2 X-ray 4R8I Se (SAD) 2.05 2015
Mammalian Thrombin aptamer Thrombin X-ray 5DO4 molecular replacement(MR) 1.86 2016
Mammalian Factor Xa-aptamer factor Xa (FXa)
factor Xa and Rivaroxaban		 X-ray 5VOE
5VOF		 molecular replacement(MR) 2.0
2.25		 2018
Mammalian Spinach RNA aptamer Fab BL3-6S97N X-ray 6B14
6B3K		 molecular replacement(MR) 1.64
2.09		 2018
Mammalian A9g RNA aptamer human glutamate carboxypeptidase II (GCPII) X-ray 6RTI molecular replacement(MR) 2.2 2020
Others Bacteriophage MS2 coat protein-aptamer bacteriophage MS2 coat protein X-ray 6MSF
5MSF,7MSF
1U1Y		 molecular replacement(MR) 2.8
2.8
2.85		 1998a
1998b
2004
Others Bovine prion protein(bPrP) aptamer prion NMR 2RQJ
2RSK
2RU7
6K84		 NA NA 2009
2013
2014
2020
Viral HIV-1 REV peptide-aptamer REV peptide NMR 1ULL
484D		 NA NA 1996
1999
Viral REX16 aptamer HTLV-1 arginine-rich Rex peptide NMR 1EXY NA NA 2000
Viral Tat aptamer HIV Tat protein NMR 1NBK NA NA 2003
Fluorophores Spinach aptamer Trifluoroethyl, Fab
1TU, Fab
bromo-ligand analog, Fab
Fab		 X-ray 4Q9R
4KZD
4Q9Q
4KZE		 molecular replacement(MR) 3.12
2.19
2.45
2.4		 2014

Nucleic acid

Category Name Ligand Structure Determination NDB Phase Determination Resolution(Å) Year
Mammalian AML1 (RUNX1)-aptamer AML1 Runt domain NMR 2RRC NA NA 2011
Viral LR06(GA) aptamer TAR RNA NMR 2OOM
2PN9		 NA NA 2007
NMR 2RN1 NA NA 2008a
X-ray 2JLT Br(SAD) 2.9 2008b
Viral RBA-14 aptamer Rev RNA X-ray 6CF2 molecular replacement(MR) 3.0 2018