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BMRB: 17449

2L9E

Solution Structure of the human Anti-codon Stem and loop(hASL) of transfer RNA Lysine III (tRNALys3)

Authors

Vendeix, F.A. P., Murphy, F.V., Leszczynska, G., Cantara, W., Gustilo, E.M., Sproat, B., Malkiewicz, A., Agris, P.F.

Assembly

tRNALys3UUU

Entity

1. tRNALys3UUU (polymer), 17 monomers, 5707.511 Da Detail

GCAGACUXUU XAUCUGC

Formula weight

5707.511 Da

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 88.2 %, Completeness: 73.7 %, Completeness (bb): 68.9 % Detail

Polymer type: polyribonucleotide

	Total	¹H
All	73.7 % (98 of 133)	73.7 % (98 of 133)
Suger, PO4	68.9 % (62 of 90)	68.9 % (62 of 90)
Nucleobase	83.7 % (36 of 43)	83.7 % (36 of 43)
Aromatic	85.7 % (30 of 35)	85.7 % (30 of 35)

1. RNA (5'-R(*GP*CP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*UP*CP*UP*GP*C)-3')

GCAGACUXUU XAUCUGC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 275 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	tRNALys3UUU	natural abundance		1.50 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 275 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
4	tRNALys3UUU	natural abundance		1.50 mM
5	D2O	natural abundance		100 %

Release date

2011-03-07

Citation

Human tRNA(Lys3)(UUU) is pre-structured by natural modifications for cognate and wobble codon binding through keto-enol tautomerism
Vendeix, F.A.P., Murphy, F.V., Cantara, W.A., Leszczyska, G., Gustilo, E.M., Sproat, B., Malkiewicz, A., Agris, P.F.
J. Mol. Biol. (2012), 416, 467-485, PubMed 22227389 , DOI 10.1016/j.jmb.2011.12.048 , Abstract

Related entities 1. tRNALys3UUU, : 1 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 275 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	tRNALys3UUU	natural abundance		1.50 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 2D 1H-1H TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	tRNALys3UUU	natural abundance		1.50 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

3 2D 1H-1H COSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K

#	Name	Isotope labeling	Type	Concentration
4	tRNALys3UUU	natural abundance		1.50 mM
5	D2O	natural abundance		100 %

4 2D DQF-COSY

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K

#	Name	Isotope labeling	Type	Concentration
4	tRNALys3UUU	natural abundance		1.50 mM
5	D2O	natural abundance		100 %

5 2D 1H-1H NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K

#	Name	Isotope labeling	Type	Concentration
4	tRNALys3UUU	natural abundance		1.50 mM
5	D2O	natural abundance		100 %

6 2D 1H-1H TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K

#	Name	Isotope labeling	Type	Concentration
4	tRNALys3UUU	natural abundance		1.50 mM
5	D2O	natural abundance		100 %

7 2D 1H-13C HSQC

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K

#	Name	Isotope labeling	Type	Concentration
4	tRNALys3UUU	natural abundance		1.50 mM
5	D2O	natural abundance		100 %

8 2D 1H-31P HETCOR

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K

#	Name	Isotope labeling	Type	Concentration
4	tRNALys3UUU	natural abundance		1.50 mM
5	D2O	natural abundance		100 %

9 2D 1H-1H NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	tRNALys3UUU	natural abundance		1.50 mM
2	H2O	natural abundance		90 %
3	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_17449_2l9e.nef
Input source #2: Coordindates	2l9e.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:7:U:O3'	1:8:70U:P	unknown	unknown	n/a
1:8:70U:O3'	1:9:U:P	unknown	unknown	n/a
1:10:U:O3'	1:11:12A:P	unknown	unknown	n/a
1:11:12A:O3'	1:12:A:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	34	70U	5-(O-METHYLACETO)-2-THIO-2-DEOXY-URIDINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	37	12A	2-METHYLTHIO-N6-(AMINOCARBONYL-L-THREONYL)-ADENOSINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--30--------40---
GCAGACUXUUXAUCUGC
|||||||||||||||||
GCAGACUXUUXAUCUGC
--------10-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	17	0	0	100.0

Content subtype: combined_17449_2l9e.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	127		100.0 (chain: A, length: 17)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	488 (1)	noe	100.0 (chain: A, length: 17)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	26 (1)	hbond	58.8 (chain: A, length: 17)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	130 (130)	.	100.0 (chain: A, length: 17)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 127
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 100.0%
- Total number of restraints: 488
- Weight of restraints: 1.0 (488)
- Potential type of restraints: square-well-parabolic (488)
- Range of distance target values: 1.57, 4.98 (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_6
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 58.8%
  - Total number of restraints: 26
  - Weight of restraints: 1.0 (26)
  - Potential type of restraints: square-well-parabolic (26)
  - 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: 17, Sequence coverage: 100.0%
- Total number of restraints: 130
- Total number of restraints per polymer type: 130
- Weight of restraints: 1.0 (130)
- Potential type of restraints: square-well-parabolic (130)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords 2-methylthio-N6-threonyl carbamoyl-adenosine, 5-methoxycarbonylmethyl-2-thiouridine, Anti-ccodon, ASL, Lysine, modified nucleotides, tRNA