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BMRB: 34133

5NWV

NMR assignment and structure of a peptide derived from the fusion peptide of HIV-1 gp41 in the presence of dodecylphosphocholine micelles

Authors

Jimenez, M.A., Serrano, S., Nieva, J.L., Huarte, N.

Assembly

scrFP-tag,Gp41

Entity

1. scrFP-tag,Gp41 (polymer, Thiol state: not present), 35 monomers, 3818.377 Da Detail

GIGAFGLLGF LAAGSKKXKN EQELLELDKW ASLWN

Formula weight

3818.377 Da

Source organism

Human immunodeficiency virus 1

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.1 %, Completeness: 80.8 %, Completeness (bb): 78.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.8 % (329 of 407)	97.2 % (205 of 211)	61.8 % (97 of 157)	69.2 % (27 of 39)
Backbone	78.9 % (161 of 204)	98.6 % (72 of 73)	67.0 % (65 of 97)	70.6 % (24 of 34)
Sidechain	84.9 % (197 of 232)	96.4 % (133 of 138)	68.5 % (61 of 89)	60.0 % (3 of 5)
Aromatic	52.3 % (23 of 44)	95.5 % (21 of 22)	0.0 % (0 of 20)	100.0 % (2 of 2)
Methyl	100.0 % (40 of 40)	100.0 % (20 of 20)	100.0 % (20 of 20)

1. entity 1

GIGAFGLLGF LAAGSKKXKN EQELLELDKW ASLWN

Show sample condition

Sample

Solvent system hexafluoroisopropanol/water, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.6 mM scrFP-tag, 25 % [U-98% 2H] HFIP, 7.5 % H2O, 67.5 % [U-99% 2H] D2O, 2 mM HEPES, 0.1 mM DSS, hexafluoroisopropanol/water.

#	Name	Isotope labeling	Type	Concentration
1	D2O	[U-99% 2H]		67.5 %
2	DSS	natural abundance		0.1 mM
3	H2O	natural abundance		7.5 %
4	HEPES	natural abundance		2 mM
5	HFIP	[U-98% 2H]		25 %
6	scrFP-tag	natural abundance		0.6 (±0.1) mM

Protein Blocks Logo

Calculated from 20 models in PDB: 5NWV, Strand ID: A Detail

Release date

2017-05-30

Citation

Structure-Related Roles for the Conservation of the HIV-1 Fusion Peptide Sequence Revealed by Nuclear Magnetic Resonance
Serrano, S., Huarte, N., Rujas, E., Andreu, D., Nieva, J.L., Jimenez, M.A.
Biochemistry (2017), 56, 5503-5511, PubMed 28930470 , DOI 10.1021/acs.biochem.7b00745 , Abstract

Related entities 1. scrFP-tag,Gp41, : 1 : 3 : 16 entities Detail

Experiments performed 5 experiments Detail

1 2D 1H-1H COSY

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system hexafluoroisopropanol/water, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.6 mM scrFP-tag, 25 % [U-98% 2H] HFIP, 7.5 % H2O, 67.5 % [U-99% 2H] D2O, 2 mM HEPES, 0.1 mM DSS, hexafluoroisopropanol/water.

#	Name	Isotope labeling	Type	Concentration
1	D2O	[U-99% 2H]		67.5 %
2	DSS	natural abundance		0.1 mM
3	H2O	natural abundance		7.5 %
4	HEPES	natural abundance		2 mM
5	HFIP	[U-98% 2H]		25 %
6	scrFP-tag	natural abundance		0.6 (±0.1) mM

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system hexafluoroisopropanol/water, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.6 mM scrFP-tag, 25 % [U-98% 2H] HFIP, 7.5 % H2O, 67.5 % [U-99% 2H] D2O, 2 mM HEPES, 0.1 mM DSS, hexafluoroisopropanol/water.

#	Name	Isotope labeling	Type	Concentration
1	D2O	[U-99% 2H]		67.5 %
2	DSS	natural abundance		0.1 mM
3	H2O	natural abundance		7.5 %
4	HEPES	natural abundance		2 mM
5	HFIP	[U-98% 2H]		25 %
6	scrFP-tag	natural abundance		0.6 (±0.1) mM

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system hexafluoroisopropanol/water, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.6 mM scrFP-tag, 25 % [U-98% 2H] HFIP, 7.5 % H2O, 67.5 % [U-99% 2H] D2O, 2 mM HEPES, 0.1 mM DSS, hexafluoroisopropanol/water.

#	Name	Isotope labeling	Type	Concentration
1	D2O	[U-99% 2H]		67.5 %
2	DSS	natural abundance		0.1 mM
3	H2O	natural abundance		7.5 %
4	HEPES	natural abundance		2 mM
5	HFIP	[U-98% 2H]		25 %
6	scrFP-tag	natural abundance		0.6 (±0.1) mM

4 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system hexafluoroisopropanol/water, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.6 mM scrFP-tag, 25 % [U-98% 2H] HFIP, 7.5 % H2O, 67.5 % [U-99% 2H] D2O, 2 mM HEPES, 0.1 mM DSS, hexafluoroisopropanol/water.

#	Name	Isotope labeling	Type	Concentration
1	D2O	[U-99% 2H]		67.5 %
2	DSS	natural abundance		0.1 mM
3	H2O	natural abundance		7.5 %
4	HEPES	natural abundance		2 mM
5	HFIP	[U-98% 2H]		25 %
6	scrFP-tag	natural abundance		0.6 (±0.1) mM

5 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system hexafluoroisopropanol/water, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.6 mM scrFP-tag, 25 % [U-98% 2H] HFIP, 7.5 % H2O, 67.5 % [U-99% 2H] D2O, 2 mM HEPES, 0.1 mM DSS, hexafluoroisopropanol/water.

#	Name	Isotope labeling	Type	Concentration
1	D2O	[U-99% 2H]		67.5 %
2	DSS	natural abundance		0.1 mM
3	H2O	natural abundance		7.5 %
4	HEPES	natural abundance		2 mM
5	HFIP	[U-98% 2H]		25 %
6	scrFP-tag	natural abundance		0.6 (±0.1) mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34133_5nwv.nef
Input source #2: Coordindates	5nwv.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)
1:17:LYS:C	1:18:ACA:N6	unknown	unknown	n/a
1:18:ACA:C1	1:19:LYS:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	18	ACA	6-AMINOHEXANOIC ACID	Assigned chemical shifts, Coordinates

Sequence alignments

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

--------10--------20--------30-----
GIGAFGLLGFLAAGSKKXKNEQELLELDKWASLWN
|||||||||||||||||||||||||||||||||||
GIGAFGLLGFLAAGSKKXKNEQELLELDKWASLWN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	35	0	0	100.0

Content subtype: combined_34133_5nwv.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	339		100.0 (chain: A, length: 35)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	386 (1)	noe	94.3 (chain: A, length: 35)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	59 (59)	.	97.1 (chain: A, length: 35)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 214
  - ¹³C chemical shifts: 97
  - ¹⁵N chemical shifts: 28
- Completeness of assignments
  - Entity_assemble_ID: A
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 94.3%
- Total number of restraints: 386
- Weight of restraints: 1.0 (386)
- Potential type of restraints: upper-bound-parabolic (386)
- Range of distance target values: 2.4, 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: 35, Sequence coverage: 97.1%
- Total number of restraints: 59
- Total number of restraints per polymer type: 59
- Weight of restraints: 1.0 (59)
- Potential type of restraints: square-well-parabolic (59)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Envelope glycoprotein gp41, STRUCTURE FROM CYANA 2.1, fusion peptide, viral protein