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Found 1 Document (0.418 seconds)

BMRB: 25603

2N2O

Structure of murine tumour necrosis factor alpha CDE RNA

Authors

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

Assembly

murine tumour necrosis factor alpha CDE RNA

Entity

1. murine tumour necrosis factor alpha CDE RNA (polymer, Thiol state: not present), 23 monomers, 7406.315 Da Detail

GCAUGUUUUC UGUGAAAACG GUU

Formula weight

7406.315 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.6 %, Completeness (bb): 95.3 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N	³¹P
All	91.6 % (359 of 392)	92.5 % (184 of 199)	95.5 % (148 of 155)	40.0 % (6 of 15)	91.3 % (21 of 23)
Suger, PO4	95.3 % (263 of 276)	97.1 % (134 of 138)	93.9 % (108 of 115)		91.3 % (21 of 23)
Nucleobase	82.8 % (96 of 116)	82.0 % (50 of 61)	100.0 % (40 of 40)	40.0 % (6 of 15)
Aromatic	83.6 % (92 of 110)	83.6 % (46 of 55)	100.0 % (40 of 40)	40.0 % (6 of 15)

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

GCAUGUUUUC UGUGAAAACG GUU

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1), Details main sample for chemical shift analysis

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPUPCPUPGPUPGPAPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]	0.30 (±0.05) mM
2	sodium phosphate	natural abundance	20 (±5.0) mM
3	D2O	[U-100% 2H]	55 M

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1), Details water sample for immino analysis

#	Name	Isotope labeling	Type	Concentration
4	RNA (5'-R(PGPCPAPUPGPUPUPUPUPCPUPGPUPGPAPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]		0.30 (±0.05) mM
5	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), Details RDC sample

#	Name	Isotope labeling	Concentration
6	RNA (5'-R(PGPCPAPUPGPUPUPUPUPCPUPGPUPGPAPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]	0.30 (±0.05) mM
7	sodium phosphate	natural abundance	20 (±5.0) mM
8	Pf1 phage	natural abundance	30 (±5.0) 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

Related entities 1. murine tumour necrosis factor alpha CDE RNA, : 1 : 2 entities Detail

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), Details main sample for chemical shift analysis

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPUPCPUPGPUPGPAPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]	0.30 (±0.05) mM
2	sodium phosphate	natural abundance	20 (±5.0) mM
3	D2O	[U-100% 2H]	55 M

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), Details main sample for chemical shift analysis

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPUPCPUPGPUPGPAPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]	0.30 (±0.05) mM
2	sodium phosphate	natural abundance	20 (±5.0) mM
3	D2O	[U-100% 2H]	55 M

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), Details water sample for immino analysis

#	Name	Isotope labeling	Type	Concentration
4	RNA (5'-R(PGPCPAPUPGPUPUPUPUPCPUPGPUPGPAPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]		0.30 (±0.05) mM
5	sodium phosphate	natural abundance		20 (±5.0) mM

4 3D-HCCH-COSY-TOCSY

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), Details main sample for chemical shift analysis

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPUPCPUPGPUPGPAPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]	0.30 (±0.05) mM
2	sodium phosphate	natural abundance	20 (±5.0) mM
3	D2O	[U-100% 2H]	55 M

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), Details main sample for chemical shift analysis

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPUPCPUPGPUPGPAPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]	0.30 (±0.05) mM
2	sodium phosphate	natural abundance	20 (±5.0) mM
3	D2O	[U-100% 2H]	55 M

6 2D HNN-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), Details main sample for chemical shift analysis

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPUPCPUPGPUPGPAPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]	0.30 (±0.05) mM
2	sodium phosphate	natural abundance	20 (±5.0) mM
3	D2O	[U-100% 2H]	55 M

7 3D 13C-edited NOESY

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), Details main sample for chemical shift analysis

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPUPCPUPGPUPGPAPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]	0.30 (±0.05) mM
2	sodium phosphate	natural abundance	20 (±5.0) mM
3	D2O	[U-100% 2H]	55 M

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), Details main sample for chemical shift analysis

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPUPCPUPGPUPGPAPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]	0.30 (±0.05) mM
2	sodium phosphate	natural abundance	20 (±5.0) mM
3	D2O	[U-100% 2H]	55 M

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

Instrument

Bruker Avance - 600 MHz cyoprobe platform

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 (±0.05) K, pH 6.5 (±0.1), Details main sample for chemical shift analysis

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPUPCPUPGPUPGPAPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]	0.30 (±0.05) mM
2	sodium phosphate	natural abundance	20 (±5.0) mM
3	D2O	[U-100% 2H]	55 M

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), Details main sample for chemical shift analysis

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPUPCPUPGPUPGPAPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]	0.30 (±0.05) mM
2	sodium phosphate	natural abundance	20 (±5.0) mM
3	D2O	[U-100% 2H]	55 M

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), Details main sample for chemical shift analysis

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(PGPCPAPUPGPUPUPUPUPCPUPGPUPGPAPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]	0.30 (±0.05) mM
2	sodium phosphate	natural abundance	20 (±5.0) mM
3	D2O	[U-100% 2H]	55 M

12 13C-base edited IPAP

Instrument

Bruker Avance - 600 MHz cyoprobe platform

Sample

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

#	Name	Isotope labeling	Concentration
6	RNA (5'-R(PGPCPAPUPGPUPUPUPUPCPUPGPUPGPAPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]	0.30 (±0.05) mM
7	sodium phosphate	natural abundance	20 (±5.0) mM
8	Pf1 phage	natural abundance	30 (±5.0) mg/mL

13 13C-sugar edited IPAP

Instrument

Bruker Avance - 600 MHz cyoprobe platform

Sample

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

#	Name	Isotope labeling	Concentration
6	RNA (5'-R(PGPCPAPUPGPUPUPUPUPCPUPGPUPGPAPAPAPAPCPGPGPUP*U)-3')	[U-100% 13C; U-100% 15N]	0.30 (±0.05) mM
7	sodium phosphate	natural abundance	20 (±5.0) mM
8	Pf1 phage	natural abundance	30 (±5.0) 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_25603_2n2o.nef
Input source #2: Coordindates	2n2o.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---
GCAUGUUUUCUGUGAAAACGGUU
|||||||||||||||||||||||
GCAUGUUUUCUGUGAAAACGGUU

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_25603_2n2o.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	387		100.0 (chain: A, length: 23)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	320 (1)	noe	100.0 (chain: A, length: 23)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	12 (1)	noe	26.1 (chain: A, length: 23)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	28 (1)	hbond	52.2 (chain: A, length: 23)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	82 (82)	.	82.6 (chain: A, length: 23)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_6	OK	49 (49)	.	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: 185
- ¹³C chemical shifts: 148
- ¹⁵N chemical shifts: 33
- ³¹P chemical shifts: 21

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	G	N9	168.53
1	G	P	-3.748
2	C	N1	151.245
3	A	N9	168.946
3	A	P	-3.622
4	U	N1	144.43
4	U	P	-3.88
5	G	N9	168.195
5	G	P	-3.538
6	U	N1	146.651
7	U	N1	146.409
7	U	P	-4.252
8	U	P	-4.119
9	U	N1	146.899
9	U	P	-4.083
10	C	N1	150.197
10	C	N3	195.532
10	C	P	-3.92
11	U	N1	144.018
11	U	P	-3.883
12	G	N9	168.003
12	G	P	-3.841
13	U	N1	143.576
13	U	P	-3.071
14	G	N9	166.724
14	G	P	-3.462
15	A	N1	220.526
15	A	N9	169.918
15	A	P	-2.905
16	A	N1	220.341
16	A	P	-3.747
17	A	H61	6.581
17	A	N1	220.357
17	A	N9	170.131
17	A	P	-3.547
18	A	N1	221.549
18	A	N9	170.604
18	A	P	-3.819
19	C	N1	149.863
19	C	N3	195.71
19	C	P	-4.078
20	G	N9	169.466
20	G	P	-3.74
21	G	N9	167.809
21	G	P	-3.954
22	U	N1	144.128
22	U	P	-3.861
23	U	N1	145.696
23	U	P	-4.079

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	199	184	92.5
¹³C chemical shifts	155	148	95.5
¹⁵N chemical shifts	15	6	40.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	138	134	97.1
¹³C chemical shifts	115	108	93.9

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	50	82.0
¹³C chemical shifts	40	40	100.0
¹⁵N chemical shifts	15	6	40.0

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: 320
- Weight of restraints: 1.0 (320)
- Potential type of restraints: square-well-parabolic (320)
- Range of distance target values: 2.4, 4.6 (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: 26.1%
  - Total number of restraints: 12
  - Weight of restraints: 1.0 (12)
  - Potential type of restraints: square-well-parabolic (12)
  - 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: Warning
    - 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: 82.6%
- 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: 49
- Potential type of restraints: undefined (49)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords CDE, NMR, RNA, murine, wild type

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Found 1 Document (0.418 seconds)

BMRB: 25603

Sample #1

Sample #2

Sample #3

Related entities 1. murine tumour necrosis factor alpha CDE RNA, : 1 : 2 entities Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 7 contents Detail