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BMRB: 18240

2LPA

Mutant of the sub-genomic promoter from Brome Mosaic Virus

Authors

Skov, J.

Assembly

Mutant of the sub-genomic promoter from Brome Mosaic Virus

Entity

1. Mutant of the sub-genomic promoter from Brome Mosaic Virus (polymer, Thiol state: not present), 15 monomers, 4855.869 Da Detail

GAGGACAUAG UCUUC

Formula weight

4855.869 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 77.2 %, Completeness (bb): 69.5 % Detail

Polymer type: polyribonucleotide

	Total	¹H	³¹P
All	77.2 % (112 of 145)	75.4 % (98 of 130)	93.3 % (14 of 15)
Suger, PO4	69.5 % (73 of 105)	65.6 % (59 of 90)	93.3 % (14 of 15)
Nucleobase	97.5 % (39 of 40)	97.5 % (39 of 40)
Aromatic	97.1 % (33 of 34)	97.1 % (33 of 34)

1. RNA (5'-R(*GP*AP*GP*GP*AP*CP*AP*UP*AP*GP*UP*CP*UP*UP*C)-3')

GAGGACAUAG UCUUC

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 2 mM RNA, 10 mM sodium phosphate buffer (pH 7), 50 mM NaCl, 2 mM EDTA

#	Name	Isotope labeling	Concentration
1	delA_RNA	natural abundance	2 mM
2	sodium phosphate	natural abundance	10 mM
3	sodium chloride	natural abundance	50 mM
4	EDTA	natural abundance	2 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Release date

2012-03-12

Citation

The subgenomic promoter of brome mosaic virus folds into a stem-loop structure capped by a pseudo-triloop that is structurally similar to the triloop of the genomic promoter
Skov, J., Gaudin, M., Podbevsek, P., Olsthoorn, R.C.L., Petersen, M.
RNA (2012), 18, 992-1000, PubMed 22393035 , DOI 10.1261/rna.029918.111 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 18239 released on 2012-03-11
Title Pseudo-triloop from the sub-genomic promoter of Brome Mosaic Virus

Related entities 1. Mutant of the sub-genomic promoter from Brome Mosaic Virus, : 1 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18240_2lpa.nef
Input source #2: Coordindates	2lpa.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

--------10-----
GAGGACAUAGUCUUC
|||||||||||||||
GAGGACAUAGUCUUC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	15	0	0	100.0

Content subtype: combined_18240_2lpa.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	114		100.0 (chain: A, length: 15)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	274 (1)	noe	100.0 (chain: A, length: 15)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	15 (1)	hbond	80.0 (chain: A, length: 15)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	128 (128)	.	100.0 (chain: A, length: 15)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 15, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 100
  - ³¹P chemical shifts: 14
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	A	P	-3.98
3	G	P	-4.24
4	G	H22	8.15
4	G	H21	6.35
4	G	P	-3.83
5	A	P	-3.66
6	C	P	-3.89
7	A	P	-3.74
8	U	P	-4.52
9	A	P	-3.44
10	G	P	-3.71
11	U	P	-5.2
12	C	P	-3.63
13	U	P	-3.63
14	U	P	-2.73
15	C	P	-3.63

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	130	98	75.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	90	59	65.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	40	39	97.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	12	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 15, Sequence coverage: 100.0%
- Total number of restraints: 274
- Weight of restraints: 1.0 (274)
- Potential type of restraints: square-well-parabolic (274)
- Range of distance target values: 2.4, 5.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 15, Sequence coverage: 80.0%
  - Total number of restraints: 15
  - Weight of restraints: 1.0 (15)
  - Potential type of restraints: square-well-parabolic (15)
  - Range of distance target values: 1.92, 1.92 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 15, Sequence coverage: 100.0%
- Total number of restraints: 128
- Total number of restraints per polymer type: 128
- Weight of restraints: 1.0 (128)
- Potential type of restraints: square-well-parabolic (128)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Brome Mosaic Virus, NMR spectroscopy, pseudo-triloop, RNA replication

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Found 1 Document (0.368 seconds)

BMRB: 18240

Sample

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Mutant of the sub-genomic promoter from Brome Mosaic Virus, : 1 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail