3EGZ | pdb_00003egz

Crystal structure of an in vitro evolved tetracycline aptamer and artificial riboswitch

PDB DOI: https://doi.org/10.2210/pdb3EGZ/pdb
NAKB: 3EGZ

Classification: RNA
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-09-11 Released: 2008-10-28
Deposition Author(s): Xiao, H., Edwards, T.E., Ferre-D'Amare, A.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.260 (Depositor), 0.265 (DCC)
R-Value Work:
0.212 (Depositor), 0.219 (DCC)
R-Value Observed:
0.217 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch

Xiao, H., Edwards, T.E., Ferre-D'Amare, A.R.

(2008) Chem Biol 15: 1125-1137

PubMed: 18940672 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.chembiol.2008.09.004
Primary Citation Related Structures:
3EGZ

PubMed Abstract:
The tetracycline aptamer is an in vitro selected RNA that binds to the antibiotic with the highest known affinity of an artificial RNA for a small molecule (Kd approximately 0.8 nM). It is one of few aptamers known to be capable of modulating gene expression in vivo. The 2.2 A resolution cocrystal structure of the aptamer reveals a pseudoknot-like fold formed by tertiary interactions between an 11 nucleotide loop and the minor groove of an irregular helix. Tetracycline binds within this interface as a magnesium ion chelate. The structure, together with previous biochemical and biophysical data, indicates that the aptamer undergoes localized folding concomitant with tetracycline binding. The three-helix junction, h-shaped architecture of this artificial RNA is more complex than those of most aptamers and is reminiscent of the structures of some natural riboswitches.

Organizational Affiliation

Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA.

Macromolecule Content

Total Structure Weight: 33.25 kDa
Atom Count: 2,298
Modeled Residue Count: 156
Deposited Residue Count: 163
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
U1 small nuclear ribonucleoprotein A	A	98	Homo sapiens	Mutation(s): 2 Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens) Explore P09012 Go to UniProtKB: P09012
PHAROS: P09012 GTEx: ENSG00000077312
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09012
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
Tetracycline aptamer and artificial riboswitch	B	65	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CTC Query on CTC Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	7-CHLOROTETRACYCLINE C₂₂ H₂₃ Cl N₂ O₈ CYDMQBQPVICBEU-XRNKAMNCSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] SDF format, chain G [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain H [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain G [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth B]	C [auth A] E [auth B] F [auth B] G [auth B] H [auth B] C [auth A], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]