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Found 1 Document (0.403 seconds)

BMRB: 26000

2NC1

Solution structure of the delta-J-delta-K domain of EMCV IRES

Authors

Imai, S., D'Souza, V., Wagner, G.

Assembly

delta-J-delta-K domain of EMCV IRES

Entity

1. delta-J-delta-K domain of EMCV IRES (polymer, Thiol state: not present), 67 monomers, 21884.04 Da Detail

GGGGCUGAAG GAUGCCCAGA GAGAUCUGGG GCCUCGGGAG AUCGAGGUUA AAAAACGUCU AGGCCCC

Formula weight

21884.04 Da

Source organism

Encephalomyocarditis virus

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 47.6 %, Completeness (bb): 41.0 % Detail

Polymer type: polyribonucleotide

	Total	¹H
All	47.6 % (274 of 576)	47.6 % (274 of 576)
Suger, PO4	41.0 % (165 of 402)	41.0 % (165 of 402)
Nucleobase	62.6 % (109 of 174)	62.6 % (109 of 174)
Aromatic	75.7 % (109 of 144)	75.7 % (109 of 144)

1. RNA (67-MER)

GGGGCUGAAG GAUGCCCAGA GAGAUCUGGG GCCUCGGGAG AUCGAGGUUA AAAAACGUCU AGGCCCC

Show sample condition

Sample

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	RNA (67-MER)	natural abundance	RNA	0.5 mM
2	potassium phosphate	natural abundance	buffer	10 mM
3	sodium chloride	natural abundance	salt	10 mM
4	D2O	[U-2H]	solvent	100 %

Release date

2016-08-07

Citation

An accurately preorganized IRES RNA structure enables eIF4G capture for initiation of viral translation
Imai, S., Hellen, C., D'Souza, V., Wagner, G.
Nat. Struct. Mol. Biol. (2016), 23, 859-864, PubMed 27525590 , DOI 10.1038/nsmb.3280 , Abstract

Experiments performed 8 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	RNA (67-MER)	natural abundance	RNA	0.5 mM
2	potassium phosphate	natural abundance	buffer	10 mM
3	sodium chloride	natural abundance	salt	10 mM
4	D2O	[U-2H]	solvent	100 %

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
10	RNA (67-MER)	[U-2H, {H1',H2',H2,H8}-Ade]	RNA	0.5 mM
11	potassium phosphate	natural abundance	buffer	10 mM
12	sodium chloride	natural abundance	salt	10 mM
13	D2O	[U-2H]	solvent	100 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
14	RNA (67-MER)	[U-2H]-Cyt, [U-2H]-Ura	RNA	0.5 mM
15	potassium phosphate	natural abundance	buffer	10 mM
16	sodium chloride	natural abundance	salt	10 mM
17	D2O	[U-2H]	solvent	100 %

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
18	RNA (67-MER)	[U-2H]-Gua, [U-2H]-Ura	RNA	0.5 mM
19	potassium phosphate	natural abundance	buffer	10 mM
20	sodium chloride	natural abundance	salt	10 mM
21	D2O	[U-2H]	solvent	100 %

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
5	RNA (67-MER)	natural abundance	RNA	0.5 mM
6	potassium phosphate	natural abundance	buffer	10 mM
7	sodium chloride	natural abundance	salt	10 mM
8	H2O	natural abundance	solvent	90 %
9	D2O	[U-2H]	solvent	10 %

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
5	RNA (67-MER)	natural abundance	RNA	0.5 mM
6	potassium phosphate	natural abundance	buffer	10 mM
7	sodium chloride	natural abundance	salt	10 mM
8	H2O	natural abundance	solvent	90 %
9	D2O	[U-2H]	solvent	10 %

7 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
22	RNA (67-MER)	[U-2H, {H1',H2',H2,H8}-Ade]	RNA	0.5 mM
23	potassium phosphate	natural abundance	buffer	10 mM
24	sodium chloride	natural abundance	salt	10 mM
25	H2O	natural abundance	solvent	90 %
26	D2O	[U-2H]	solvent	10 %

8 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
22	RNA (67-MER)	[U-2H, {H1',H2',H2,H8}-Ade]	RNA	0.5 mM
23	potassium phosphate	natural abundance	buffer	10 mM
24	sodium chloride	natural abundance	salt	10 mM
25	H2O	natural abundance	solvent	90 %
26	D2O	[U-2H]	solvent	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_26000_2nc1.nef
Input source #2: Coordindates	2nc1.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

680-----690-------700------730-------740-------770-------780-------
GGGGCUGAAGGAUGCCCAGAGAGAUCUGGGGCCUCGGGAGAUCGAGGUUAAAAAACGUCUAGGCCCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GGGGCUGAAGGAUGCCCAGAGAGAUCUGGGGCCUCGGGAGAUCGAGGUUAAAAAACGUCUAGGCCCC
--------10--------20--------30--------40--------50--------60-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	67	0	0	100.0

Content subtype: combined_26000_2nc1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	274		100.0 (chain: A, length: 67)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	506 (1)	noe	98.5 (chain: A, length: 67)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	183 (1)	hbond	88.1 (chain: A, length: 67)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	310 (310)	.	88.1 (chain: A, length: 67)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 67, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 274
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	576	274	47.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	402	165	41.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	174	109	62.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	59	59	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 67, Sequence coverage: 98.5%
- Total number of restraints: 506
- Weight of restraints: 1.0 (506)
- Potential type of restraints: square-well-parabolic (506)
- Range of distance target values: 2.15, 8.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 67, Sequence coverage: 88.1%
  - Total number of restraints: 183
  - Weight of restraints: 1.0 (183)
  - Potential type of restraints: square-well-parabolic (183)
  - Range of distance target values: 1.86, 7.3 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 67, Sequence coverage: 88.1%
- Total number of restraints: 310
- Total number of restraints per polymer type: 310
- Weight of restraints: 1.0 (310)
- Potential type of restraints: square-well-parabolic (310)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords IRES, Viral RNA, translation initiation

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Found 1 Document (0.403 seconds)

BMRB: 26000

Sample

Experiments performed 8 experiments Detail

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NMR combined restraints 5 contents Detail