BMRB Entry 50268

Title:
Small Molecule Targeting IRES Domain Inhibits Enterovirus 71 Replication via an Allosteric Mechanism that Stabilizes a Ternary Complex
Deposition date:
2020-05-10
Original release date:
2020-06-10
Authors:
Davila-Calderon, Jesse; Patwardhan, Neeraj; Chiu, Liang-Yuan; Sugarman, Andrew; Cai, Zhengguo; Penutmutchu, Srinivasa; Li, Mei-Ling; Brewer, Gary; Hargrove, Amanda; Tolbert, Blanton
Citation:

Citation: Davila-Calderon, Jesse; Patwardhan, Neeraj; Chiu, Liang-Yuan; Sugarman, Andrew; Cai, Zhengguo; Penutmutchu, Srinivasa; Li, Mei-Ling; Brewer, Gary; Hargrove, Amanda; Tolbert, Blanton. "IRES-targeting small molecule inhibits enterovirus 71 replication via allosteric stabilization of a ternary complex"  Nat. Commun. 11, 4775-4775 (2020).
PubMed: 32963221

Assembly members:

Assembly members:
entity_1, polymer, 41 residues, Formula weight is not available

Natural source:

Natural source:   Common Name: Enterovirus A71   Taxonomy ID: 138948   Superkingdom: Viruses   Kingdom: not available   Genus/species: Enterovirus Enterovirus A71

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGAUCAAUAGCAGGUGUGGC ACACCAGUCAUACCUUGAUC C

Data sets:
Data typeCount
1H chemical shifts119

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1EV71 RNA(41-MER)1

Entities:

Entity 1, EV71 RNA(41-MER) 41 residues - Formula weight is not available

1   GGAUCAAUAG
2   CAGGUGUGGC
3   ACACCAGUCA
4   UACCUUGAUC
5   C

Samples:

sample_1: rNTP, [Selective Deuteration; Fully Deuteration for U and C; Selective Deuteration for A and G with 2H at (3',4',5'5'')], 200 ± 10 uM; DMA135 800 ± 40 uM

sample_2: rNTP, [Selective Deuteration; EQUIMOLAR MIX:ATP, GTP, CTP, UTP], 200 ± 10 uM

sample_3: rNTP, [Selective Deuteration; Fully Deuteration for U and C; Selective Deuteration for A and G with 2H at (3',4',5'5'')], 200 ± 10 uM

sample_4: rNTP, [Selective Deuteration; EQUIMOLAR MIX:ATP, GTP, CTP, UTP], 200 ± 10 uM; DMA135 800 ± 40 uM

sample_conditions_1: ionic strength: 20 mM; pH: 6.5; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_4isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_1

Software:

AMBER - refinement

NMRFAM-SPARKY - chemical shift assignment

HADDOCK - Docking

TOPSPIN - collection

NMRViewJ - chemical shift assignment

NMRPipe - processing

NMRDraw - processing

NMR spectrometers:

  • Bruker Avance 700 MHz
  • Bruker Avance 900 MHz
  • Bruker Avance 800 MHz