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BMRB: 26034

2NCS

NMR assignment and structure of a peptide derived from the membrane proximal external region of HIV-1 gp41 in the presence of dodecylphosphocholine micelles

Authors

Jimenez, M., Nieva, J.L., Rujas, E., Partida-Hanon, A., Bruix, M.

Assembly

membrane proximal external region of HIV-1 gp41 in DPC micelles

Entity

1. membrane proximal external region of HIV-1 gp41 in DPC micelles (polymer, Thiol state: not present), 36 monomers, 4613.597 Da Detail

KKKKDKWASL WNWFDITNWL WYIKLFIMIV GKKKKK

Formula weight

4613.597 Da

Source organism

Human immunodeficiency virus 1

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 71.6 %, Completeness (bb): 74.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	71.6 % (348 of 486)	91.1 % (256 of 281)	44.9 % (92 of 205)
Backbone	74.4 % (134 of 180)	98.6 % (72 of 73)	57.9 % (62 of 107)
Sidechain	69.5 % (237 of 341)	88.5 % (184 of 208)	39.8 % (53 of 133)
Aromatic	45.8 % (38 of 83)	86.4 % (38 of 44)	0.0 % (0 of 39)
Methyl	100.0 % (36 of 36)	100.0 % (18 of 18)	100.0 % (18 of 18)

1. 10E8p

KKKKDKWASL WNWFDITNWL WYIKLFIMIV GKKKKK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	10E8p	natural abundance	protein	0.5 mM
2	DPC	[U-2H]		20 mM
3	HEPES	natural abundance	buffer	2 mM
4	DSS	natural abundance		0.1 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	10E8p	natural abundance	protein	0.5 mM
8	DPC	[U-2H]		20 mM
9	HEPES	natural abundance	buffer	2 mM
10	DSS	natural abundance		0.1 mM
11	D2O	[U-2H]	solvent	100 %

Protein Blocks Logo

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

Release date

2016-04-18

Citation

Structural basis for broad neutralization of HIV-1 through the molecular recognition of 10E8 helical epitope at the membrane interface
Rujas, E., Partida-Hanon, A., Gulzar, N., Morante, K., Apellaniz, B., Garcia-Porras, M., Bruix, M., Tsumoto, K., Scott, J.K., Jimenez, M.K., Caaveiro, J.MM., Nieva, J.L.
Sci. Rep. (2016), 6, 38177-38177, PubMed 27905530 , DOI 10.1038/srep38177 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 26035 released on 2016-04-18
Title NMR assignment and structure of a peptide derived from the membrane proximal external region of HIV-1 gp41 in the presence of hexafluoroisopropanol

Related entities 1. membrane proximal external region of HIV-1 gp41 in DPC micelles, : 1 : 1 : 1 : 26 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_26034_2ncs.nef
Input source #2: Coordindates	2ncs.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--------30------
KKKKDKWASLWNWFDITNWLWYIKLFIMIVGKKKKK
||||||||||||||||||||||||||||||||||||
KKKKDKWASLWNWFDITNWLWYIKLFIMIVGKKKKK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	36	0	0	100.0

Content subtype: combined_26034_2ncs.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	343		100.0 (chain: A, length: 36)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	612 (1)	noe	100.0 (chain: A, length: 36)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 256
  - ¹³C chemical shifts: 87
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	281	256	91.1
¹³C chemical shifts	205	87	42.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	72	98.6
¹³C chemical shifts	72	35	48.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	208	184	88.5
¹³C chemical shifts	133	52	39.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	19	100.0
¹³C chemical shifts	19	19	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	38	86.4
¹³C chemical shifts	39	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 100.0%
- Total number of restraints: 612
- Weight of restraints: 1.0 (612)
- Potential type of restraints: upper-bound-parabolic (612)
- Range of distance target values: 2.13, 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

Keywords HIV-1 gp41 protein, neutralizing epitope, peptide, peptide vaccine

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Found 1 Document (0.689 seconds)

BMRB: 26034

Sample #1

Sample #2

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. membrane proximal external region of HIV-1 gp41 in DPC micelles, : 1 : 1 : 1 : 26 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

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Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail