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BMRB: 19583

2MG3

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

Serrano, S., Apellaniz, B., Huarte, N., Nieva, J.L., Jimenez, M.

Assembly

peptide derived from the membrane proximal external region of HIV-1 gp41

Entity

1. peptide derived from the membrane proximal external region of HIV-1 gp41 (polymer, Thiol state: not present), 28 monomers, 3483.258 Da Detail

KKKNWFDITN WLWYIKLFIM IVGGLVKK

Formula weight

3483.258 Da

Source organism

Human immunodeficiency virus

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 61.1 %, Completeness (bb): 40.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	61.1 % (223 of 365)	97.6 % (203 of 208)	12.7 % (20 of 157)
Backbone	40.0 % (56 of 140)	96.6 % (56 of 58)	0.0 % (0 of 82)
Sidechain	66.5 % (167 of 251)	98.0 % (147 of 150)	19.8 % (20 of 101)
Aromatic	52.5 % (32 of 61)	100.0 % (32 of 32)	0.0 % (0 of 29)
Methyl	100.0 % (38 of 38)	100.0 % (19 of 19)	100.0 % (19 of 19)

1. CpreTM

KKKNWFDITN WLWYIKLFIM IVGGLVKK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	CpreTM	natural abundance	0.5 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %
4	DPC	[U-99% 2H]	20 mM
5	HEPES	natural abundance	2 mM
6	DSS	natural abundance	0.1 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2MG3, Strand ID: A Detail

Release date

2015-03-22

Citation

The Atomic Structure of the HIV-1 gp41 Transmembrane Domain and its Connection to the Inmmunogenic Membrane-proximal External Region
Serrano, S., Apellaniz, B., Huarte, N., Jimenez, M., Nieva, J.L.
Not known

Related entities 1. peptide derived from the membrane proximal external region of HIV-1 gp41, : 1 : 1 : 88 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19583_2mg3.nef
Input source #2: Coordindates	2mg3.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--------
KKKNWFDITNWLWYIKLFIMIVGGLVKK
||||||||||||||||||||||||||||
KKKNWFDITNWLWYIKLFIMIVGGLVKK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	28	0	0	100.0

Content subtype: combined_19583_2mg3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	223		100.0 (chain: A, length: 28)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	374 (1)	noe	96.4 (chain: A, length: 28)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	47 (47)	.	100.0 (chain: A, length: 28)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 203
  - ¹³C chemical shifts: 20
- 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	208	203	97.6
¹³C chemical shifts	157	20	12.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	56	96.6
¹³C chemical shifts	56	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	150	147	98.0
¹³C chemical shifts	101	20	19.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	20	100.0
¹³C chemical shifts	20	20	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	32	100.0
¹³C chemical shifts	29	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 96.4%
- Total number of restraints: 374
- Weight of restraints: 1.0 (374)
- Potential type of restraints: upper-bound-parabolic (374)
- Range of distance target values: 2.55, 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: 28, Sequence coverage: 100.0%
- Total number of restraints: 47
- Total number of restraints per polymer type: 47
- Weight of restraints: 1.0 (47)
- Potential type of restraints: square-well-parabolic (47)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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

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Found 1 Document (0.55 seconds)

BMRB: 19583

Sample

Related entities 1. peptide derived from the membrane proximal external region of HIV-1 gp41, : 1 : 1 : 88 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail