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BMRB: 15915

2K7E

NMR structure of the human tRNALys3 bound to the HIV genome Loop I

Authors

Bilbille, Y., Vendeix, F.P.A., Guenther, R., Malkiewicz, A., Ariza, X., Vilarrasa, J., Agris, P.

Assembly

5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3'

Entity

1. RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3') (polymer, Thiol state: not present), 12 monomers, 3978.380 Da Detail

GCGGUGUAAA AG

2. T-RNA (5'-R(*CP*UP*(2SU)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3') (polymer, Thiol state: not present), 12 monomers, 3686.233 Da Detail

CUXUUAAXCU GC

Total weight

7664.613 Da

Max. entity weight

3978.38 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 91.7 %, Completeness: 59.5 %, Completeness (bb): 45.5 % Detail

Polymer type: polyribonucleotide

	Total	¹H
All	59.5 % (113 of 190)	59.5 % (113 of 190)
Suger, PO4	45.5 % (60 of 132)	45.5 % (60 of 132)
Nucleobase	91.4 % (53 of 58)	91.4 % (53 of 58)
Aromatic	94.0 % (47 of 50)	94.0 % (47 of 50)

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

GCGGUGUAAA AG

2. T-RNA (5'-R(*CP*UP*(2SU)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3')

CUXUUAAXCU GC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 276 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPCPGPGPUPGPUPAPAPAPAPG)-3')	natural abundance	0.3-1.2 mM
2	T-RNA (5'-R(CPUP(2SU)PUPUPAPAP(PSU)PCPUPGPC)-3')	natural abundance	0.3-1.2 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	100 mM
5	H2O	natural abundance	90 %
6	D2O	[U-100% 2H]	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 276 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	RNA (5'-R(GPCPGPGPUPGPUPAPAPAPAPG)-3')	natural abundance	0.3-1.2 mM
8	T-RNA (5'-R(CPUP(2SU)PUPUPAPAP(PSU)PCPUPGPC)-3')	natural abundance	0.3-1.2 mM
9	sodium phosphate	natural abundance	10 mM
10	sodium chloride	natural abundance	100 mM
11	D2O	[U-100% 2H]	100 %

Chem. Shift Complete2

Sequence coverage: 50.0 %, Completeness: 44.5 %, Completeness (bb): 34.5 % Detail

Polymer type: polyribonucleotide

	Total	¹H
All	44.5 % (169 of 380)	44.5 % (169 of 380)
Suger, PO4	34.5 % (91 of 264)	34.5 % (91 of 264)
Nucleobase	67.2 % (78 of 116)	67.2 % (78 of 116)
Aromatic	70.0 % (70 of 100)	70.0 % (70 of 100)

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

GCGGUGUAAA AG

2. T-RNA (5'-R(*CP*UP*(2SU)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3')

CUXUUAAXCU GC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 276 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPCPGPGPUPGPUPAPAPAPAPG)-3')	natural abundance	0.3-1.2 mM
2	T-RNA (5'-R(CPUP(2SU)PUPUPAPAP(PSU)PCPUPGPC)-3')	natural abundance	0.3-1.2 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	100 mM
5	H2O	natural abundance	90 %
6	D2O	[U-100% 2H]	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 276 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	RNA (5'-R(GPCPGPGPUPGPUPAPAPAPAPG)-3')	natural abundance	0.3-1.2 mM
8	T-RNA (5'-R(CPUP(2SU)PUPUPAPAP(PSU)PCPUPGPC)-3')	natural abundance	0.3-1.2 mM
9	sodium phosphate	natural abundance	10 mM
10	sodium chloride	natural abundance	100 mM
11	D2O	[U-100% 2H]	100 %

Chem. Shift Complete3

Sequence coverage: 41.7 %, Completeness: 39.6 %, Completeness (bb): 30.3 % Detail

Polymer type: polyribonucleotide

	Total	¹H
All	39.6 % (226 of 570)	39.6 % (226 of 570)
Suger, PO4	30.3 % (120 of 396)	30.3 % (120 of 396)
Nucleobase	60.9 % (106 of 174)	60.9 % (106 of 174)
Aromatic	62.7 % (94 of 150)	62.7 % (94 of 150)

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

GCGGUGUAAA AG

2. T-RNA (5'-R(*CP*UP*(2SU)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3')

CUXUUAAXCU GC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 276 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPCPGPGPUPGPUPAPAPAPAPG)-3')	natural abundance	0.3-1.2 mM
2	T-RNA (5'-R(CPUP(2SU)PUPUPAPAP(PSU)PCPUPGPC)-3')	natural abundance	0.3-1.2 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	100 mM
5	H2O	natural abundance	90 %
6	D2O	[U-100% 2H]	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 276 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	RNA (5'-R(GPCPGPGPUPGPUPAPAPAPAPG)-3')	natural abundance	0.3-1.2 mM
8	T-RNA (5'-R(CPUP(2SU)PUPUPAPAP(PSU)PCPUPGPC)-3')	natural abundance	0.3-1.2 mM
9	sodium phosphate	natural abundance	10 mM
10	sodium chloride	natural abundance	100 mM
11	D2O	[U-100% 2H]	100 %

Release date

2008-09-29

Citation

The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs
Bilbille, Y., Vendeix, F.A.P., Guenther, R., Malkiewicz, A., Ariza, X., Vilarrasa, J., Agris, P.F.
Nucleic Acids Res. (2009), 37, 3342-3353, PubMed 19324888 , DOI 10.1093/nar/gkp187 , Abstract

Related entities 1. RNA (5'-R(GPCPGPGPUPGPUPAPAPAPAPG)-3'), : 1 entities Detail

Experiments performed 6 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 276 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPCPGPGPUPGPUPAPAPAPAPG)-3')	natural abundance	0.3-1.2 mM
2	T-RNA (5'-R(CPUP(2SU)PUPUPAPAP(PSU)PCPUPGPC)-3')	natural abundance	0.3-1.2 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	100 mM
5	H2O	natural abundance	90 %
6	D2O	[U-100% 2H]	10 %

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPCPGPGPUPGPUPAPAPAPAPG)-3')	natural abundance	0.3-1.2 mM
2	T-RNA (5'-R(CPUP(2SU)PUPUPAPAP(PSU)PCPUPGPC)-3')	natural abundance	0.3-1.2 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	100 mM
5	H2O	natural abundance	90 %
6	D2O	[U-100% 2H]	10 %

3 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	RNA (5'-R(GPCPGPGPUPGPUPAPAPAPAPG)-3')	natural abundance	0.3-1.2 mM
8	T-RNA (5'-R(CPUP(2SU)PUPUPAPAP(PSU)PCPUPGPC)-3')	natural abundance	0.3-1.2 mM
9	sodium phosphate	natural abundance	10 mM
10	sodium chloride	natural abundance	100 mM
11	D2O	[U-100% 2H]	100 %

4 2D DQF-COSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	RNA (5'-R(GPCPGPGPUPGPUPAPAPAPAPG)-3')	natural abundance	0.3-1.2 mM
8	T-RNA (5'-R(CPUP(2SU)PUPUPAPAP(PSU)PCPUPGPC)-3')	natural abundance	0.3-1.2 mM
9	sodium phosphate	natural abundance	10 mM
10	sodium chloride	natural abundance	100 mM
11	D2O	[U-100% 2H]	100 %

5 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	RNA (5'-R(GPCPGPGPUPGPUPAPAPAPAPG)-3')	natural abundance	0.3-1.2 mM
8	T-RNA (5'-R(CPUP(2SU)PUPUPAPAP(PSU)PCPUPGPC)-3')	natural abundance	0.3-1.2 mM
9	sodium phosphate	natural abundance	10 mM
10	sodium chloride	natural abundance	100 mM
11	D2O	[U-100% 2H]	100 %

6 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 276 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPCPGPGPUPGPUPAPAPAPAPG)-3')	natural abundance	0.3-1.2 mM
2	T-RNA (5'-R(CPUP(2SU)PUPUPAPAP(PSU)PCPUPGPC)-3')	natural abundance	0.3-1.2 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	100 mM
5	H2O	natural abundance	90 %
6	D2O	[U-100% 2H]	10 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15915_2k7e.nef
Input source #2: Coordindates	2k7e.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)
2:2:U:O3'	2:3:SUR:P	unknown	unknown	n/a
2:3:SUR:O3'	2:4:U:P	unknown	unknown	n/a
2:7:A:O3'	2:8:PSU:P	unknown	unknown	n/a
2:8:PSU:O3'	2:9:C:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	3	SUR	1-(BETA-D-RIBOFURANOSYL)-2-THIO-URACIL-5'-PHOSPHATE	Assigned chemical shifts, Distance restraints, Coordinates
B	8	PSU	PSEUDOURIDINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Coordinates

Sequence alignments

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

--------10--
GCGGUGUAAAAG
||||||||||||
GCGGUGUAAAAG

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

--------10--
CUXUUAAXCUGC
||||||||||||
CUXUUAAXCUGC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	12	0	0	100.0
B	B	12	0	0	100.0

Content subtype: combined_15915_2k7e.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	126		100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)
2	Assigned chemical shifts	assigned_chem_shift_list_2	OK	56		100.0 (chain: A, length: 12)
3	Assigned chemical shifts	assigned_chem_shift_list_3	Warning	70		100.0 (chain: B, length: 12)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	266 (1)	noe	100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	46 (1)	hbond	83.3 (chain: A, length: 12), 83.3 (chain: B, length: 12)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 126
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts
Saveframe: assigned_chem_shift_list_2
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 56
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
Saveframe: assigned_chem_shift_list_3
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 70
- Completeness of assignments
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	100	56	56.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	31	43.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	25	89.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	13	12	92.3

Comp_index_ID	Comp_ID
3	SUR

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	102	64	62.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	67	33	49.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	31	88.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	100	56	56.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	31	43.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	25	89.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	13	12	92.3

Comp_index_ID	Comp_ID
3	SUR

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	102	64	62.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	67	33	49.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	31	88.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
- Total number of restraints: 266
- Weight of restraints: 1.0 (266)
- Potential type of restraints: square-well-parabolic (266)
- Range of distance target values: 1.4, 2.85 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- 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: 12, Sequence coverage: 83.3%
    - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 83.3%
  - Total number of restraints: 46
  - Weight of restraints: 1.0 (46)
  - Potential type of restraints: square-well-parabolic (46)
  - Range of distance target values: 1.67, 2.95 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Keywords 2-thiouridine, HIV, modifications, NMR, pseudouridine, PSU, RNA, S2U, tRNALys3

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Found 1 Document (0.51 seconds)

BMRB: 15915

Sample #1

Sample #2

Sample #1

Sample #2

Sample #1

Sample #2

Related entities 1. RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3'), : 1 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail

Related entities 1. RNA (5'-R(GPCPGPGPUPGPUPAPAPAPAPG)-3'), : 1 entities Detail