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Found 1 Document (0.357 seconds)

BMRB: 31008

7UMC

DENV1 SLA RNA (DenvSLATL)

Authors

Sun, Y.T., Varani, G., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Assembly

RNA (70-MER)

Entity

1. RNA (70-MER) (polymer, Thiol state: not present), 70 monomers, 22677.44 Da Detail

GGAGUGGUUA GUCUACGUGG ACCGACAAGA CUUCGGUCGA AUCGGAAGGA AACUUAACGU AGUUCUAACC

Formula weight

22677.44 Da

Source organism

dengue virus type I

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 77.1 %, Completeness: 23.0 %, Completeness (bb): 11.0 % Detail

Polymer type: polyribonucleotide

	Total	¹H
All	23.0 % (139 of 604)	23.0 % (139 of 604)
Suger, PO4	11.0 % (46 of 420)	11.0 % (46 of 420)
Nucleobase	50.5 % (93 of 184)	50.5 % (93 of 184)
Aromatic	47.4 % (74 of 156)	47.4 % (74 of 156)

1. entity 1

GGAGUGGUUA GUCUACGUGG ACCGACAAGA CUUCGGUCGA AUCGGAAGGA AACUUAACGU AGUUCUAACC

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM RNA (70-MER), 10 mM potassium phosphate, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	RNA (70-MER)	natural abundance		1 mM
2	potassium phosphate	natural abundance		10 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM [U-2H] RNA (70-MER), 10 mM potassium phosphate, 100% D2O

#	Name	Isotope labeling	Type	Concentration
3	RNA (70-MER)	[U-2H]		1 mM
4	potassium phosphate	natural abundance		10 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM RNA (70-MER), 10 mM potassium phosphate, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	RNA (70-MER)	natural abundance		1 mM
6	potassium phosphate	natural abundance		10 mM

Release date

2022-05-02

Citation

Structure of the Dengue Virus RNA Promoter
Sun, Y.T., Varani, G.
RNA (2022), 28, 1210-1223, PubMed 35750488 , DOI 10.1261/rna.079197.122 , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 31009 released on 2022-05-08
    Title DENV1 SLA three-way junction RNA (DenvSLAsh)
  BMRB: 30853 released on 2021-02-13
    Title Denv1 5'UTR Stem3

Related entities 1. RNA (70-MER), : 1 : 1 entities Detail

Experiments performed 5 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr31008_3.str
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

Content subtype: bmr31008_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	185		77.1 (chain: 1, length: 70)
1	Chemical shift references	chem_shift_reference_1	OK	1		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 70, Sequence coverage: 77.1%

--------10--------20--------30--------40--------50--------60--------70
GGAGUGGUUAGUCUACGUGGACCGACAAGACUUCGGUCGAAUCGGAAGGAAACUUAACGUAGUUCUAACC
      ||||||||||||   ||||||||||||||||||  ||||| |    ||||||||||||||||||
......GUUAGUCUACGU...CCGACAAGACUUCGGUCG..UCGGA.G....CUUAACGUAGUUCUAACC

Total number of assignments
- ¹H chemical shifts: 185

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
7	G	HO2'	4.413
8	U	HO2'	4.41
9	U	HO2'	4.388
10	A	HO2'	4.6
11	G	HO2'	4.403
12	U	HO2'	4.175
13	C	HO2'	4.174
14	U	HO2'	4.467
15	A	HO2'	4.418
16	C	HO2'	4.373
17	G	HO2'	4.307
22	C	HO2'	4.415
23	C	HO2'	4.578
24	G	HO2'	4.601
25	A	HO2'	4.067
26	C	HO2'	3.99
27	A	HO2'	4.442
28	A	HO2'	4.764
32	U	HO2'	3.679
33	U	HO2'	4.578
34	C	HO2'	4.01
35	G	HO2'	4.732
36	G	HO2'	4.521
37	U	HO2'	4.577
38	C	HO2'	4.277
39	G	HO2'	4.829
42	U	HO2'	4.282
43	C	HO2'	4.464
44	G	HO2'	4.573
45	G	HO2'	4.628
53	C	HO2'	4.586
54	U	HO2'	4.253
55	U	HO2'	4.357
56	A	HO2'	4.34
57	A	HO2'	4.603
59	G	HO2'	4.299
60	U	HO2'	4.519
61	A	HO2'	4.454
62	G	HO2'	4.206
63	U	HO2'	4.306
64	U	HO2'	4.442
65	C	HO2'	4.34
66	U	HO2'	4.554
67	A	HO2'	4.445
68	A	HO2'	4.36
69	C	HO2'	3.982

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	604	139	23.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	420	46	11.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	184	93	50.5

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	29	48.3

Histogram of normalized assigned chemical shifts

Keywords 5' UTR, NS5 promoter, RNA, SLA, flavivirus, viral replication

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Found 1 Document (0.357 seconds)

BMRB: 31008

Sample #1

Sample #2

Sample #3

Entries sharing articles BMRB: 2 entries Detail

Related entities 1. RNA (70-MER), : 1 : 1 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail