BMRBj - BMREntryMaster

Found 1 Document (0.326 seconds)

BMRB: 34553

7A3Y

RNA duplex with a cytosine bulge in complex with berberine

Authors

Podbevsek, P., Plavec, J.

Assembly

RNA-A chain A, RNA-A chain B

Entity

1. RNA-A chain A, RNA-A chain B, entity 1 (polymer, Thiol state: not present), 13 monomers, 4172.450 Da Detail

GCAGCUCGUC CUG

2. RNA-A chain A, RNA-A chain B, entity 2 (polymer, Thiol state: not present), 12 monomers, 3914.332 Da Detail

CAGGAUAGCU GC

3. RNA-A chain A, RNA-A chain B, entity BER (non-polymer), 336.361 Da

Total weight

8423.144 Da

Max. entity weight

4172.45 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 43.4 %, Completeness (bb): 18.0 % Detail

Polymer type: polyribonucleotide

	Total	¹H
All	43.4 % (96 of 221)	43.4 % (96 of 221)
Suger, PO4	18.0 % (27 of 150)	18.0 % (27 of 150)
Nucleobase	97.2 % (69 of 71)	97.2 % (69 of 71)
Aromatic	96.4 % (53 of 55)	96.4 % (53 of 55)

1. entity 1

GCAGCUCGUC CUG

2. entity 2

CAGGAUAGCU GC

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.3 mM RNA-A chain A, 0.3 mM RNA-A chain B, 100 mM sodium chloride, 10 mM sodium phosphate, 1 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	RNA-A chain A	natural abundance	0.3 mM
2	RNA-A chain B	natural abundance	0.3 mM
3	sodium chloride	natural abundance	100 mM
4	sodium phosphate	natural abundance	10 mM
5	EDTA	natural abundance	1 mM

Release date

2020-09-09

Citation

Interaction between berberine and RNA for the exploration of phytochemicals role
Podbevsek, P., Plavec, J.

Related entities 1. RNA-A chain A, RNA-A chain B, entity 1, : 1 entities Detail

Related entities 2. RNA-A chain A, RNA-A chain B, entity 2, : 1 : 33 entities Detail

Experiments performed 2 experiments Detail

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34553_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

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
3	1	BER	BERBERINE	Assigned chemical shifts

Content subtype: bmr34553_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	116		100.0 (chain: 1, length: 13), 100.0 (chain: 2, length: 12), 100.0 (chain: 3, length: 1)
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: 13, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: 3, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 116
- Completeness of assignments
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 2
  - Entity_assemble_ID: 3
- Histogram of normalized assigned chemical shifts

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	117	51	43.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	78	14	17.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	39	37	94.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
7	A	H61	7.241
7	A	H62	6.196

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	104	45	43.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	13	18.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	32	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	10	100.0

Comp_index_ID	Comp_ID
1	BER

Keywords RNA, berberine, cytosine bulge

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Found 1 Document (0.326 seconds)

BMRB: 34553

Sample

Related entities 1. RNA-A chain A, RNA-A chain B, entity 1, : 1 entities Detail

Related entities 2. RNA-A chain A, RNA-A chain B, entity 2, : 1 : 33 entities Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

Chemical shift validation 5 contents Detail