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BMRB: 18852

2M1A

HIV-1 Rev ARM peptide (residues T34-R50)

Authors

Casu, F., Duggan, B.M., Hennig, M.

Assembly

HIV-1 Rev ARM peptide (residues T34-R50)

Entity

1. HIV-1 Rev ARM peptide (residues T34-R50) (polymer, Thiol state: not present), 26 monomers, 3208.638 Da Detail

GAMATRQARR NRRRRWRERQ RAAAAR

Formula weight

3208.638 Da

Exptl. method

Refine. method

torsion angle dynamics, TORSION ANGLE DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.2 %, Completeness: 92.3 %, Completeness (bb): 95.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.3 % (288 of 312)	91.9 % (158 of 172)	91.8 % (101 of 110)	96.7 % (29 of 30)
Backbone	95.5 % (149 of 156)	94.3 % (50 of 53)	96.1 % (74 of 77)	96.2 % (25 of 26)
Sidechain	90.6 % (164 of 181)	90.8 % (108 of 119)	89.7 % (52 of 58)	100.0 % (4 of 4)
Aromatic	83.3 % (10 of 12)	83.3 % (5 of 6)	80.0 % (4 of 5)	100.0 % (1 of 1)
Methyl	100.0 % (16 of 16)	100.0 % (8 of 8)	100.0 % (8 of 8)

1. Rev ARM peptide

GAMATRQARR NRRRRWRERQ RAAAAR

Show sample condition

Sample #1

Solvent system trifluoroethanol/water, Temperature 283 K, pH 7.4, Details Uniformly 15N labelled sample

#	Name	Isotope labeling	Type	Concentration
1	Rev ARM peptide	[U-15N]		1.0 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		150 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		1 mM
6	sodium azide	natural abundance		0.02 %
7	D2O	[U-99% 2H]		10.0 %
8	H2O	natural abundance		40.0 %
9	TFE	natural abundance		50.0 %

Sample #2

Solvent system trifluoroethanol/water, Temperature 283 K, pH 7.4, Details Uniformly 15N,13C labelled sample

#	Name	Isotope labeling	Type	Concentration
10	Rev ARM peptide	[U-13C; U-15N]		1.0 mM
11	sodium phosphate	natural abundance		50 mM
12	potassium chloride	natural abundance		150 mM
13	EDTA	natural abundance		1 mM
14	DTT	natural abundance		1 mM
15	sodium azide	natural abundance		0.02 %
16	D2O	[U-99% 2H]		10.0 %
17	H2O	natural abundance		40.0 %
18	TFE	[U-99% 2H]		50.0 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2M1A, Strand ID: A Detail

Release date

2013-09-03

Citation

The arginine-rich RNA-binding motif of HIV-1 Rev is intrinsically disordered and folds upon RRE binding
Casu, F., Duggan, B.M., Hennig, M.
Biophys. J. (2013), 105, 1004-1017, PubMed 23972852 , DOI 10.1016/j.bpj.2013.07.022 , Abstract

Related entities 1. HIV-1 Rev ARM peptide (residues T34-R50), : 1 entities Detail

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz Equipped with a 5mm 1H[13C/15N] triple resonance probe featuring cryogenically cooled preamplifiers and r.f. coils on 1H and 13C channels and z-axis gradient

Sample

State isotropic, Solvent system trifluoroethanol/water, Temperature 283 K, pH 7.4, Details Uniformly 15N labelled sample

#	Name	Isotope labeling	Type	Concentration
1	Rev ARM peptide	[U-15N]		1.0 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		150 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		1 mM
6	sodium azide	natural abundance		0.02 %
7	D2O	[U-99% 2H]		10.0 %
8	H2O	natural abundance		40.0 %
9	TFE	natural abundance		50.0 %

2 2D 1H-15N HSQC NH2 only

Instrument

Bruker Avance - 800 MHz Equipped with a 5mm 1H[13C/15N] triple resonance probe featuring cryogenically cooled preamplifiers and r.f. coils on 1H and 13C channels and z-axis gradient

Sample

State isotropic, Solvent system trifluoroethanol/water, Temperature 283 K, pH 7.4, Details Uniformly 15N labelled sample

#	Name	Isotope labeling	Type	Concentration
1	Rev ARM peptide	[U-15N]		1.0 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		150 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		1 mM
6	sodium azide	natural abundance		0.02 %
7	D2O	[U-99% 2H]		10.0 %
8	H2O	natural abundance		40.0 %
9	TFE	natural abundance		50.0 %

3 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz Equipped with a 5mm 1H[13C/15N] triple resonance probe featuring cryogenically cooled preamplifiers and r.f. coils on 1H and 13C channels and z-axis gradient

Sample

State isotropic, Solvent system trifluoroethanol/water, Temperature 283 K, pH 7.4, Details Uniformly 15N,13C labelled sample

#	Name	Isotope labeling	Type	Concentration
10	Rev ARM peptide	[U-13C; U-15N]		1.0 mM
11	sodium phosphate	natural abundance		50 mM
12	potassium chloride	natural abundance		150 mM
13	EDTA	natural abundance		1 mM
14	DTT	natural abundance		1 mM
15	sodium azide	natural abundance		0.02 %
16	D2O	[U-99% 2H]		10.0 %
17	H2O	natural abundance		40.0 %
18	TFE	[U-99% 2H]		50.0 %

4 3D HNCO

Instrument

Bruker Avance - 800 MHz Equipped with a 5mm 1H[13C/15N] triple resonance probe featuring cryogenically cooled preamplifiers and r.f. coils on 1H and 13C channels and z-axis gradient

Sample

State isotropic, Solvent system trifluoroethanol/water, Temperature 283 K, pH 7.4, Details Uniformly 15N,13C labelled sample

#	Name	Isotope labeling	Type	Concentration
10	Rev ARM peptide	[U-13C; U-15N]		1.0 mM
11	sodium phosphate	natural abundance		50 mM
12	potassium chloride	natural abundance		150 mM
13	EDTA	natural abundance		1 mM
14	DTT	natural abundance		1 mM
15	sodium azide	natural abundance		0.02 %
16	D2O	[U-99% 2H]		10.0 %
17	H2O	natural abundance		40.0 %
18	TFE	[U-99% 2H]		50.0 %

5 3D HNCA

Instrument

Bruker Avance - 800 MHz Equipped with a 5mm 1H[13C/15N] triple resonance probe featuring cryogenically cooled preamplifiers and r.f. coils on 1H and 13C channels and z-axis gradient

Sample

State isotropic, Solvent system trifluoroethanol/water, Temperature 283 K, pH 7.4, Details Uniformly 15N,13C labelled sample

#	Name	Isotope labeling	Type	Concentration
10	Rev ARM peptide	[U-13C; U-15N]		1.0 mM
11	sodium phosphate	natural abundance		50 mM
12	potassium chloride	natural abundance		150 mM
13	EDTA	natural abundance		1 mM
14	DTT	natural abundance		1 mM
15	sodium azide	natural abundance		0.02 %
16	D2O	[U-99% 2H]		10.0 %
17	H2O	natural abundance		40.0 %
18	TFE	[U-99% 2H]		50.0 %

6 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz Equipped with a 5mm 1H[13C/15N] triple resonance probe featuring cryogenically cooled preamplifiers and r.f. coils on 1H and 13C channels and z-axis gradient

Sample

State isotropic, Solvent system trifluoroethanol/water, Temperature 283 K, pH 7.4, Details Uniformly 15N,13C labelled sample

#	Name	Isotope labeling	Type	Concentration
10	Rev ARM peptide	[U-13C; U-15N]		1.0 mM
11	sodium phosphate	natural abundance		50 mM
12	potassium chloride	natural abundance		150 mM
13	EDTA	natural abundance		1 mM
14	DTT	natural abundance		1 mM
15	sodium azide	natural abundance		0.02 %
16	D2O	[U-99% 2H]		10.0 %
17	H2O	natural abundance		40.0 %
18	TFE	[U-99% 2H]		50.0 %

7 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz Equipped with a 5mm 1H[13C/15N] triple resonance probe featuring cryogenically cooled preamplifiers and r.f. coils on 1H and 13C channels and z-axis gradient

Sample

State isotropic, Solvent system trifluoroethanol/water, Temperature 283 K, pH 7.4, Details Uniformly 15N,13C labelled sample

#	Name	Isotope labeling	Type	Concentration
10	Rev ARM peptide	[U-13C; U-15N]		1.0 mM
11	sodium phosphate	natural abundance		50 mM
12	potassium chloride	natural abundance		150 mM
13	EDTA	natural abundance		1 mM
14	DTT	natural abundance		1 mM
15	sodium azide	natural abundance		0.02 %
16	D2O	[U-99% 2H]		10.0 %
17	H2O	natural abundance		40.0 %
18	TFE	[U-99% 2H]		50.0 %

8 3D HNCACB

Instrument

Bruker Avance - 800 MHz Equipped with a 5mm 1H[13C/15N] triple resonance probe featuring cryogenically cooled preamplifiers and r.f. coils on 1H and 13C channels and z-axis gradient

Sample

State isotropic, Solvent system trifluoroethanol/water, Temperature 283 K, pH 7.4, Details Uniformly 15N,13C labelled sample

#	Name	Isotope labeling	Type	Concentration
10	Rev ARM peptide	[U-13C; U-15N]		1.0 mM
11	sodium phosphate	natural abundance		50 mM
12	potassium chloride	natural abundance		150 mM
13	EDTA	natural abundance		1 mM
14	DTT	natural abundance		1 mM
15	sodium azide	natural abundance		0.02 %
16	D2O	[U-99% 2H]		10.0 %
17	H2O	natural abundance		40.0 %
18	TFE	[U-99% 2H]		50.0 %

9 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz Equipped with a 5mm 1H[13C/15N] triple resonance probe featuring cryogenically cooled preamplifiers and r.f. coils on 1H and 13C channels and z-axis gradient

Sample

State isotropic, Solvent system trifluoroethanol/water, Temperature 283 K, pH 7.4, Details Uniformly 15N,13C labelled sample

#	Name	Isotope labeling	Type	Concentration
10	Rev ARM peptide	[U-13C; U-15N]		1.0 mM
11	sodium phosphate	natural abundance		50 mM
12	potassium chloride	natural abundance		150 mM
13	EDTA	natural abundance		1 mM
14	DTT	natural abundance		1 mM
15	sodium azide	natural abundance		0.02 %
16	D2O	[U-99% 2H]		10.0 %
17	H2O	natural abundance		40.0 %
18	TFE	[U-99% 2H]		50.0 %

10 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz Equipped with a 5mm 1H[13C/15N] triple resonance probe featuring cryogenically cooled preamplifiers and r.f. coils on 1H and 13C channels and z-axis gradient

Sample

State isotropic, Solvent system trifluoroethanol/water, Temperature 283 K, pH 7.4, Details Uniformly 15N,13C labelled sample

#	Name	Isotope labeling	Type	Concentration
10	Rev ARM peptide	[U-13C; U-15N]		1.0 mM
11	sodium phosphate	natural abundance		50 mM
12	potassium chloride	natural abundance		150 mM
13	EDTA	natural abundance		1 mM
14	DTT	natural abundance		1 mM
15	sodium azide	natural abundance		0.02 %
16	D2O	[U-99% 2H]		10.0 %
17	H2O	natural abundance		40.0 %
18	TFE	[U-99% 2H]		50.0 %

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz Equipped with a 5mm 1H[13C/15N] triple resonance probe featuring cryogenically cooled preamplifiers and r.f. coils on 1H and 13C channels and z-axis gradient

Sample

State isotropic, Solvent system trifluoroethanol/water, Temperature 283 K, pH 7.4, Details Uniformly 15N labelled sample

#	Name	Isotope labeling	Type	Concentration
1	Rev ARM peptide	[U-15N]		1.0 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		150 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		1 mM
6	sodium azide	natural abundance		0.02 %
7	D2O	[U-99% 2H]		10.0 %
8	H2O	natural abundance		40.0 %
9	TFE	natural abundance		50.0 %

12 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz Equipped with a 5mm 1H[13C/15N] triple resonance probe featuring cryogenically cooled preamplifiers and r.f. coils on 1H and 13C channels and z-axis gradient

Sample

State isotropic, Solvent system trifluoroethanol/water, Temperature 283 K, pH 7.4, Details Uniformly 15N,13C labelled sample

#	Name	Isotope labeling	Type	Concentration
10	Rev ARM peptide	[U-13C; U-15N]		1.0 mM
11	sodium phosphate	natural abundance		50 mM
12	potassium chloride	natural abundance		150 mM
13	EDTA	natural abundance		1 mM
14	DTT	natural abundance		1 mM
15	sodium azide	natural abundance		0.02 %
16	D2O	[U-99% 2H]		10.0 %
17	H2O	natural abundance		40.0 %
18	TFE	[U-99% 2H]		50.0 %

13 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz Equipped with a 5mm 1H[13C/15N] triple resonance probe featuring cryogenically cooled preamplifiers and r.f. coils on 1H and 13C channels and z-axis gradient

Sample

State isotropic, Solvent system trifluoroethanol/water, Temperature 283 K, pH 7.4, Details Uniformly 15N,13C labelled sample

#	Name	Isotope labeling	Type	Concentration
10	Rev ARM peptide	[U-13C; U-15N]		1.0 mM
11	sodium phosphate	natural abundance		50 mM
12	potassium chloride	natural abundance		150 mM
13	EDTA	natural abundance		1 mM
14	DTT	natural abundance		1 mM
15	sodium azide	natural abundance		0.02 %
16	D2O	[U-99% 2H]		10.0 %
17	H2O	natural abundance		40.0 %
18	TFE	[U-99% 2H]		50.0 %

14 3D HNHA

Instrument

Bruker Avance - 800 MHz Equipped with a 5mm 1H[13C/15N] triple resonance probe featuring cryogenically cooled preamplifiers and r.f. coils on 1H and 13C channels and z-axis gradient

Sample

State isotropic, Solvent system trifluoroethanol/water, Temperature 283 K, pH 7.4, Details Uniformly 15N labelled sample

#	Name	Isotope labeling	Type	Concentration
1	Rev ARM peptide	[U-15N]		1.0 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		150 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		1 mM
6	sodium azide	natural abundance		0.02 %
7	D2O	[U-99% 2H]		10.0 %
8	H2O	natural abundance		40.0 %
9	TFE	natural abundance		50.0 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18852_2m1a.nef
Input source #2: Coordindates	2m1a.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------
GAMATRQARRNRRRRWRERQRAAAAR
||||||||||||||||||||||||||
GAMATRQARRNRRRRWRERQRAAAAR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	26	0	0	100.0

Content subtype: combined_18852_2m1a.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	284		96.2 (chain: A, length: 26)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	318 (1)	noe	92.3 (chain: A, length: 26)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	48 (48)	.	100.0 (chain: A, length: 26)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 26, Sequence coverage: 96.2%
- Total number of assignments
  - ¹H chemical shifts: 156
  - ¹³C chemical shifts: 100
  - ¹⁵N chemical shifts: 28
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 26, Sequence coverage: 92.3%
- Total number of restraints: 317
- Weight of restraints: 1.0 (317)
- Potential type of restraints: upper-bound-parabolic (317)
- Range of distance target values: 2.72, 5.5 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 26, Sequence coverage: 100.0%
- Total number of restraints: 48
- Total number of restraints per polymer type: 48
- Weight of restraints: 1.0 (48)
- Potential type of restraints: square-well-parabolic (48)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords arginine-rich motif, HIV, Rev