BMRB Entry 50268

Name: Small Molecule Targeting IRES Domain Inhibits Enterovirus 71 Replication via an Allosteric Mechanism that Stabilizes a Ternary Complex
Published: 2020-06-10

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PDB ID: 6xb7
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50268
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Small Molecule Targeting IRES Domain Inhibits Enterovirus 71 Replication via an Allosteric Mechanism that Stabilizes a Ternary Complex PubMed: 32963221

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: 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).

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

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

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: GGAUCAAUAGCAGGUGUGGC ACACCAGUCAUACCUUGAUC C

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	119

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	EV71 RNA(41-MER)	1

Entities:

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

1

G

A

U

C

A

U

A

G

2

C

A

G

U

G

U

G

C

3

A

C

A

C

A

G

U

C

A

4

U

A

C

U

G

A

U

C

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:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3	isotropic	sample_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