BMRBj - BMREntryMaster

Found 1 Document (0.363 seconds)

BMRB: 25604

2N2P

Solution structure of a double base-pair inversion mutant of murine tumour necrosis factor alpha CDE-23 RNA

Authors

Codutti, L., Leppek, K., Zalesak, J., Windeisen, V., Masiewicz, P., Stoecklin, G., Carlomagno, T.

Assembly

double base-pair inversion mutant of murine tumour necrosis factor alpha CDE-23 RNA

Entity

1. double base-pair inversion mutant of murine tumour necrosis factor alpha CDE-23 RNA (polymer, Thiol state: not present), 23 monomers, 7406.315 Da Detail

GCAUGUUUAG UGUCUAAACG GUU

Formula weight

7406.315 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.6 %, Completeness (bb): 96.7 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	³¹P
All	93.6 % (353 of 377)	90.5 % (180 of 199)	97.4 % (151 of 155)	95.7 % (22 of 23)
Suger, PO4	96.7 % (267 of 276)	97.1 % (134 of 138)	96.5 % (111 of 115)	95.7 % (22 of 23)
Nucleobase	85.1 % (86 of 101)	75.4 % (46 of 61)	100.0 % (40 of 40)
Aromatic	90.5 % (86 of 95)	83.6 % (46 of 55)	100.0 % (40 of 40)

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

GCAUGUUUAG UGUCUAAACG GUU

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPAPGPUPGPUPCPUPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]		0.35 (±0.05) mM
2	sodium phosphate	natural abundance		20 (±5.0) mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
3	RNA (5'-R(PGPCPAPUPGPUPUPUPAPGPUPGPUPCPUPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]		0.35 (±0.05) mM
4	sodium phosphate	natural abundance		20 (±5.0) mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
5	RNA (5'-R(PGPCPAPUPGPUPUPUPAPGPUPGPUPCPUPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]	0.35 (±0.05) mM
6	sodium phosphate	natural abundance	20 (±5.0) mM
7	Pf1 phage	natural abundance	30 mg/mL

Release date

2015-08-02

Citation

A Distinct, Sequence-Induced Conformation Is Required for Recognition of the Constitutive Decay Element RNA by Roquin
Codutti, L., Leppek, K., Zalesak, J., Windeisen, V., Masiewicz, P., Stoecklin, G., Carlomagno, T.
Structure (2015), 23, 1437-1447, PubMed 26165594 , DOI 10.1016/j.str.2015.06.001 , Abstract

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPAPGPUPGPUPCPUPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]		0.35 (±0.05) mM
2	sodium phosphate	natural abundance		20 (±5.0) mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPAPGPUPGPUPCPUPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]		0.35 (±0.05) mM
2	sodium phosphate	natural abundance		20 (±5.0) mM

3 immino-1H-1H NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
3	RNA (5'-R(PGPCPAPUPGPUPUPUPAPGPUPGPUPCPUPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]		0.35 (±0.05) mM
4	sodium phosphate	natural abundance		20 (±5.0) mM

4 3D-HCCH-COSY-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPAPGPUPGPUPCPUPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]		0.35 (±0.05) mM
2	sodium phosphate	natural abundance		20 (±5.0) mM

5 3D HsCNb/HbCNb

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPAPGPUPGPUPCPUPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]		0.35 (±0.05) mM
2	sodium phosphate	natural abundance		20 (±5.0) mM

6 2D HNN-COSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
3	RNA (5'-R(PGPCPAPUPGPUPUPUPAPGPUPGPUPCPUPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]		0.35 (±0.05) mM
4	sodium phosphate	natural abundance		20 (±5.0) mM

7 3D 13C-edited NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPAPGPUPGPUPCPUPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]		0.35 (±0.05) mM
2	sodium phosphate	natural abundance		20 (±5.0) mM

8 2D COSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPAPGPUPGPUPCPUPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]		0.35 (±0.05) mM
2	sodium phosphate	natural abundance		20 (±5.0) mM

9 1H-31P HET-COR(P,H-COSY-H,C-HMQC)

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPAPGPUPGPUPCPUPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]		0.35 (±0.05) mM
2	sodium phosphate	natural abundance		20 (±5.0) mM

10 T1-13C-EDIT relaxation

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPAPGPUPGPUPCPUPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]		0.35 (±0.05) mM
2	sodium phosphate	natural abundance		20 (±5.0) mM

11 T1rho-13C-EDIT relaxation

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPAPGPUPGPUPCPUPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]		0.35 (±0.05) mM
2	sodium phosphate	natural abundance		20 (±5.0) mM

12 13C-base edited IPAP

Instrument

Bruker Avance - 800 MHz

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
5	RNA (5'-R(PGPCPAPUPGPUPUPUPAPGPUPGPUPCPUPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]	0.35 (±0.05) mM
6	sodium phosphate	natural abundance	20 (±5.0) mM
7	Pf1 phage	natural abundance	30 mg/mL

13 13C-sugar edited IPAP

Instrument

Bruker Avance - 800 MHz

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
5	RNA (5'-R(PGPCPAPUPGPUPUPUPAPGPUPGPUPCPUPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]	0.35 (±0.05) mM
6	sodium phosphate	natural abundance	20 (±5.0) mM
7	Pf1 phage	natural abundance	30 mg/mL

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_25604_2n2p.nef
Input source #2: Coordindates	2n2p.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--------20---
GCAUGUUUAGUGUCUAAACGGUU
|||||||||||||||||||||||
GCAUGUUUAGUGUCUAAACGGUU

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	23	0	0	100.0

Content subtype: combined_25604_2n2p.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	353		100.0 (chain: A, length: 23)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	346 (1)	noe	100.0 (chain: A, length: 23)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	30 (1)	noe	69.6 (chain: A, length: 23)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	28 (1)	hbond	52.2 (chain: A, length: 23)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	82 (82)	.	78.3 (chain: A, length: 23)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_6	OK	47 (47)	.	95.7 (chain: A, length: 23)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: A, Chain length: 23, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 180
- ¹³C chemical shifts: 151
- ³¹P chemical shifts: 22

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	C	P	-3.833
3	A	P	-3.858
4	U	P	-3.924
5	G	P	-3.569
6	U	P	-3.665
7	U	P	-3.899
8	U	P	-4.155
9	A	P	-3.879
10	G	P	-3.762
11	U	P	-3.896
12	G	P	-3.629
13	U	P	-3.2
14	C	P	-3.595
15	U	P	-3.137
16	A	P	-3.653
17	A	P	-3.823
18	A	P	-4.058
19	C	P	-4.023
20	G	P	-3.735
21	G	P	-3.924
22	U	P	-3.8
23	U	P	-2.938

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	199	180	90.5
¹³C chemical shifts	155	151	97.4

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	138	134	97.1
¹³C chemical shifts	115	111	96.5

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	46	75.4
¹³C chemical shifts	40	40	100.0

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	16	16	100.0
¹³C chemical shifts	16	16	100.0

Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 23, Sequence coverage: 100.0%
- Total number of restraints: 346
- Weight of restraints: 1.0 (346)
- Potential type of restraints: square-well-parabolic (346)
- Range of distance target values: 2.4, 4.5 (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: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 23, Sequence coverage: 69.6%
  - Total number of restraints: 30
  - Weight of restraints: 1.0 (30)
  - Potential type of restraints: square-well-parabolic (30)
  - Range of distance target values: 2.4, 4.5 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_5
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 23, Sequence coverage: 52.2%
    - Total number of restraints: 28
    - Weight of restraints: 1.0 (28)
    - Potential type of restraints: square-well-parabolic (28)
    - Range of distance target values: 1.71, 3.08 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 23, Sequence coverage: 78.3%
- Total number of restraints: 82
- Total number of restraints per polymer type: 82
- Weight of restraints: 1.0 (82)
- Potential type of restraints: square-well-parabolic (82)
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 23, Sequence coverage: 95.7%
- Total number of restraints: 47
- Potential type of restraints: undefined (47)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords CDE, NMR, RNA, murine, mutant

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.363 seconds)

BMRB: 25604

Sample #1

Sample #2

Sample #3

Experiments performed 13 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail