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BMRB: 19545

2MFD

The Solution Structure of a cGCUUAg RNA Pentaloop from Bovine Enterovirus Vir404/03

Authors

Ihle, Y., Zell, R., Gorlach, M.

Assembly

cGCUUAg RNA Pentaloop from Bovine Enterovirus Vir404/03

Entity

1. cGCUUAg RNA Pentaloop from Bovine Enterovirus Vir404/03 (polymer, Thiol state: not present), 19 monomers, 6133.604 Da Detail

GGCGUUCGCU UAGAACGUC

Formula weight

6133.604 Da

Source organism

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.8 %, Completeness (bb): 98.1 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	93.8 % (286 of 305)	96.4 % (161 of 167)	98.4 % (125 of 127)	0.0 % (0 of 11)
Suger, PO4	98.1 % (205 of 209)	98.2 % (112 of 114)	97.9 % (93 of 95)
Nucleobase	84.4 % (81 of 96)	92.5 % (49 of 53)	100.0 % (32 of 32)	0.0 % (0 of 11)
Aromatic	84.9 % (73 of 86)	95.3 % (41 of 43)	100.0 % (32 of 32)	0.0 % (0 of 11)

1. BEVSLD5

GGCGUUCGCU UAGAACGUC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	BEVSLD5	natural abundance		1.1 mM
2	potassium phosphate	natural abundance		10 mM
3	potassium chloride	natural abundance		40 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
7	BEVSLD5	[U-100% 13C; U-100% 15N]		0.9 mM
8	potassium phosphate	natural abundance		10 mM
9	potassium chloride	natural abundance		40 mM
10	EDTA	natural abundance		0.2 mM
11	D2O	natural abundance		100 %

Release date

2014-10-12

Citation

The Solution Structure of a cGCUUAg RNA Pentaloop from Bovine Enterovirus Vir 404/03
Ihle, Y., Zell, R., Gorlach, M.
Not known

Related entities 1. cGCUUAg RNA Pentaloop from Bovine Enterovirus Vir404/03, : 1 entities Detail

Experiments performed 15 experiments Detail

1 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	BEVSLD5	natural abundance		1.1 mM
2	potassium phosphate	natural abundance		10 mM
3	potassium chloride	natural abundance		40 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	BEVSLD5	natural abundance		1.1 mM
2	potassium phosphate	natural abundance		10 mM
3	potassium chloride	natural abundance		40 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 2D 1H-1H COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	BEVSLD5	natural abundance		1.1 mM
2	potassium phosphate	natural abundance		10 mM
3	potassium chloride	natural abundance		40 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	BEVSLD5	natural abundance		1.1 mM
2	potassium phosphate	natural abundance		10 mM
3	potassium chloride	natural abundance		40 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 2D DQF-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	BEVSLD5	natural abundance		1.1 mM
2	potassium phosphate	natural abundance		10 mM
3	potassium chloride	natural abundance		40 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

6 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	BEVSLD5	natural abundance		1.1 mM
2	potassium phosphate	natural abundance		10 mM
3	potassium chloride	natural abundance		40 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 2D HcncH + 2D HccH-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
7	BEVSLD5	[U-100% 13C; U-100% 15N]		0.9 mM
8	potassium phosphate	natural abundance		10 mM
9	potassium chloride	natural abundance		40 mM
10	EDTA	natural abundance		0.2 mM
11	D2O	natural abundance		100 %

8 2D HcnH + 2D HccH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
7	BEVSLD5	[U-100% 13C; U-100% 15N]		0.9 mM
8	potassium phosphate	natural abundance		10 mM
9	potassium chloride	natural abundance		40 mM
10	EDTA	natural abundance		0.2 mM
11	D2O	natural abundance		100 %

9 3D HCCH-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
7	BEVSLD5	[U-100% 13C; U-100% 15N]		0.9 mM
8	potassium phosphate	natural abundance		10 mM
9	potassium chloride	natural abundance		40 mM
10	EDTA	natural abundance		0.2 mM
11	D2O	natural abundance		100 %

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
7	BEVSLD5	[U-100% 13C; U-100% 15N]		0.9 mM
8	potassium phosphate	natural abundance		10 mM
9	potassium chloride	natural abundance		40 mM
10	EDTA	natural abundance		0.2 mM
11	D2O	natural abundance		100 %

11 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
7	BEVSLD5	[U-100% 13C; U-100% 15N]		0.9 mM
8	potassium phosphate	natural abundance		10 mM
9	potassium chloride	natural abundance		40 mM
10	EDTA	natural abundance		0.2 mM
11	D2O	natural abundance		100 %

12 2D 1H-1H NOESY

Instrument

Bruker Avance - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	BEVSLD5	natural abundance		1.1 mM
2	potassium phosphate	natural abundance		10 mM
3	potassium chloride	natural abundance		40 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

13 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
7	BEVSLD5	[U-100% 13C; U-100% 15N]		0.9 mM
8	potassium phosphate	natural abundance		10 mM
9	potassium chloride	natural abundance		40 mM
10	EDTA	natural abundance		0.2 mM
11	D2O	natural abundance		100 %

14 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
7	BEVSLD5	[U-100% 13C; U-100% 15N]		0.9 mM
8	potassium phosphate	natural abundance		10 mM
9	potassium chloride	natural abundance		40 mM
10	EDTA	natural abundance		0.2 mM
11	D2O	natural abundance		100 %

15 2D 1H-1H TOCSY

Instrument

Bruker Avance - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	BEVSLD5	natural abundance		1.1 mM
2	potassium phosphate	natural abundance		10 mM
3	potassium chloride	natural abundance		40 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19545_2mfd.nef
Input source #2: Coordindates	2mfd.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

----60--------70---
GGCGUUCGCUUAGAACGUC
|||||||||||||||||||
GGCGUUCGCUUAGAACGUC
--------10---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	19	0	0	100.0

Content subtype: combined_19545_2mfd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	339		100.0 (chain: A, length: 19)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	664 (1)	noe	100.0 (chain: A, length: 19)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	36 (1)	hbond	73.7 (chain: A, length: 19)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	167 (167)	.	100.0 (chain: A, length: 19)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 190
- ¹³C chemical shifts: 132
- ¹⁵N chemical shifts: 17

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
55	G	HO2'	6.856
55	G	N9	169.205
56	G	H21	6.218
56	G	H22	6.218
56	G	HO2'	7.097
56	G	N9	170.268
57	C	HO2'	6.45
57	C	N1	150.606
58	G	H21	5.996
58	G	H22	5.996
58	G	HO2'	6.841
58	G	N9	168.742
59	U	HO2'	6.915
60	U	HO2'	6.69
60	U	C2	152.805
60	U	N1	147.02
61	C	HO2'	6.544
61	C	N1	150.679
62	G	H21	5.874
62	G	H22	5.874
62	G	HO2'	6.975
62	G	C4	158.62
63	C	N1	152.436
64	U	C2	154.42
64	U	N1	143.419
65	U	C2	154.37
65	U	N1	143.858
66	A	HO2'	6.349
66	A	C4	151.893
66	A	N9	168.729
67	G	H22	7.909
67	G	H21	6.149
67	G	HO2'	6.573
67	G	N9	169.943
68	A	H61	6.557
68	A	H62	7.808
68	A	HO2'	6.661
68	A	N9	170.465
69	A	H61	6.606
69	A	H62	8.1
69	A	HO2'	6.732
69	A	N9	171.056
70	C	HO2'	6.449
70	C	N1	149.918
71	G	H21	6.037
71	G	H22	6.037
71	G	HO2'	6.897
71	G	N9	169.352
72	U	HO2'	7.347
72	U	C2	154.8
72	U	N1	145.541
73	C	C2	159.565
73	C	N1	150.899

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	167	161	96.4
¹³C chemical shifts	127	125	98.4
¹⁵N chemical shifts	11	0	0.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	114	112	98.2
¹³C chemical shifts	95	93	97.9

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	53	49	92.5
¹³C chemical shifts	32	32	100.0
¹⁵N chemical shifts	11	0	0.0

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	12	12	100.0
¹³C chemical shifts	12	12	100.0

Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 100.0%
- Total number of restraints: 664
- Weight of restraints: 1.0 (664)
- Potential type of restraints: square-well-parabolic (664)
- Range of distance target values: 1.8, 4.15 (Å)
- Histogram of distance target values
- Histogram of discrepancy in 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: 19, Sequence coverage: 73.7%
  - Total number of restraints: 36
  - Weight of restraints: 1.0 (36)
  - Potential type of restraints: square-well-parabolic (36)
  - Range of distance target values: 1.9, 2.85 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 100.0%
- Total number of restraints: 167
- Total number of restraints per polymer type: 167
- Weight of restraints: 1.0 (167)
- Potential type of restraints: square-well-parabolic (167)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords 5'-NTR, bovine enterovirus, cloverleaf, pentaloop, RNA