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Found 1 Document (0.348 seconds)

BMRB: 25996

2NBX

Solution structure of the J-K region of EMCV IRES

Authors

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

Assembly

J-K region of EMCV IRES

Entity

1. J-K region of EMCV IRES (polymer, Thiol state: not present), 108 monomers, 34901.58 Da Detail

GGGGCUGAAG GAUGCCCAGA AGGUACCCCA UUGUAUGGGA UCUGAUCUGG GGCCUCGGUG CACAUGCUUU ACAUGUGUUU AGUCGAGGUU AAAAAACGUC UAGGCCCC

Formula weight

34901.58 Da

Source organism

Encephalomyocarditis virus

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 22.2 %, Completeness: 9.6 %, Completeness (bb): 6.9 % Detail

Polymer type: polyribonucleotide

	Total	¹H
All	9.6 % (90 of 939)	9.6 % (90 of 939)
Suger, PO4	6.9 % (45 of 648)	6.9 % (45 of 648)
Nucleobase	15.5 % (45 of 291)	15.5 % (45 of 291)
Aromatic	18.5 % (45 of 243)	18.5 % (45 of 243)

1. RNA (108-MER)

GGGGCUGAAG GAUGCCCAGA AGGUACCCCA UUGUAUGGGA UCUGAUCUGG GGCCUCGGUG CACAUGCUUU ACAUGUGUUU AGUCGAGGUU AAAAAACGUC UAGGCCCC

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Type	Concentration
1	RNA (108-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 %

Sample #2

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

#	Name	Isotope labeling	Type	Concentration
5	RNA (108-MER)	[U-2H, {H1',H2',H2,H8}-Ade]	RNA	0.5 mM
6	potassium phosphate	natural abundance	buffer	10 mM
7	sodium chloride	natural abundance	salt	10 mM
8	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 2 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25996_2nbx.nef
Input source #2: Coordindates	2nbx.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-------710-------720-------730-------740-------750-------760-------770-------78
GGGGCUGAAGGAUGCCCAGAAGGUACCCCAUUGUAUGGGAUCUGAUCUGGGGCCUCGGUGCACAUGCUUUACAUGUGUUUAGUCGAGGUUAAAAAACGUC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GGGGCUGAAGGAUGCCCAGAAGGUACCCCAUUGUAUGGGAUCUGAUCUGGGGCCUCGGUGCACAUGCUUUACAUGUGUUUAGUCGAGGUUAAAAAACGUC
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------
UAGGCCCC
||||||||
UAGGCCCC
--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	108	0	0	100.0

Content subtype: combined_25996_2nbx.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	90		22.2 (chain: A, length: 108)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	829 (1)	noe	99.1 (chain: A, length: 108)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	300 (1)	hbond	83.3 (chain: A, length: 108)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	579 (579)	.	96.3 (chain: A, length: 108)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 22.2%
- Total number of assignments
  - ¹H chemical shifts: 90
- Completeness of assignments
- Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 99.1%
- Total number of restraints: 829
- Weight of restraints: 1.0 (829)
- Potential type of restraints: square-well-parabolic (829)
- Range of distance target values: 1.95, 10.0 (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: 108, Sequence coverage: 83.3%
  - Total number of restraints: 300
  - Weight of restraints: 1.0 (300)
  - Potential type of restraints: square-well-parabolic (300)
  - Range of distance target values: 1.61, 7.51 (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: 108, Sequence coverage: 96.3%
- Total number of restraints: 579
- Total number of restraints per polymer type: 579
- Weight of restraints: 1.0 (579)
- Potential type of restraints: square-well-parabolic (579)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords IRES, Viral RNA, translation initiation

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Found 1 Document (0.348 seconds)

BMRB: 25996

Sample #1

Sample #2

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail