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BMRB: 30503

6E8W

MPER-TM Domain of HIV-1 envelope glycoprotein (Env)

Authors

Fu, Q., Shaik, M.M., Cai, Y., Ghantous, F., Piai, A., Peng, H., Rits-Volloch, S., Liu, Z., Harrison, S.C., Seaman, M.S., Chen, B., Chou, J.J.

Assembly

Envelope glycoprotein gp160

Entity

1. Envelope glycoprotein gp160 (polymer, Thiol state: not present), 51 monomers, 6174.330 × 3 Da Detail

LLELDKWASL WNWFDITNWL WYIRIFIIIV GSLIGLRIVF AVLSLVNRVR Q

Total weight

18522.99 Da

Max. entity weight

6174.33 Da

Source organism

Human immunodeficiency virus 1

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.0 %, Completeness: 28.7 %, Completeness (bb): 61.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	28.7 % (193 of 673)	14.9 % (51 of 343)	34.4 % (93 of 270)	81.7 % (49 of 60)
Backbone	61.4 % (188 of 306)	47.1 % (49 of 104)	59.6 % (90 of 151)	96.1 % (49 of 51)
Sidechain	1.7 % (7 of 416)	0.8 % (2 of 239)	3.0 % (5 of 168)	0.0 % (0 of 9)
Aromatic	0.0 % (0 of 98)	0.0 % (0 of 49)	0.0 % (0 of 44)	0.0 % (0 of 5)
Methyl	4.3 % (4 of 94)	4.3 % (2 of 47)	4.3 % (2 of 47)

1. entity 1

LLELDKWASL WNWFDITNWL WYIRIFIIIV GSLIGLRIVF AVLSLVNRVR Q

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 15N, 2H Envelope glycoprotein gp160, 50 mM DMPC, 100 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DMPC	natural abundance	50 mM
2	DHPC	natural abundance	100 mM
3	Envelope glycoprotein gp160	15N, 2H

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 15N, 2H, 13C Envelope glycoprotein gp160, 50 mM DMPC, 100 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	DMPC	natural abundance	50 mM
5	DHPC	natural abundance	100 mM
6	Envelope glycoprotein gp160	[U-13C; U-15N; U-2H]

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 15N, 13C Envelope glycoprotein gp160, 50 mM [U-99% 2H] DMPC, 100 mM [U-99% 2H] DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	DMPC	[U-99% 2H]	50 mM
8	DHPC	[U-99% 2H]	100 mM
9	Envelope glycoprotein gp160	[U-100% 13C; U-100% 15N]

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 15N, 2H mixed with 13C(15%) Envelope glycoprotein gp160, 50 mM [U-99% 2H] DMPC, 100 mM [U-99% 2H] DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
10	DMPC	[U-99% 2H]	50 mM
11	DHPC	[U-99% 2H]	100 mM
12	Envelope glycoprotein gp160	15N, 2H mixed with 13C(15%)

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 15N, 2H mixed with 13C Envelope glycoprotein gp160, 50 mM [U-99% 2H] DMPC, 100 mM [U-99% 2H] DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	DMPC	[U-99% 2H]	50 mM
14	DHPC	[U-99% 2H]	100 mM
15	Envelope glycoprotein gp160	15N, 2H mixed with 13C

Release date

2018-08-27

Citation

Structure of the membrane proximal external region of HIV-1 envelope glycoprotein
Fu, Q., Shaik, M.M., Cai, Y., Ghantous, F., Piai, A., Peng, H., Rits-Volloch, S., Liu, Z., Harrison, S.C., Seaman, M.S., Chen, B., Chou, J.J.
Proc. Natl. Acad. Sci. U. S. A. (2018), 115, E8892-E8899, PubMed 30185554 , DOI 10.1073/pnas.1807259115 , Abstract

Related entities 1. Envelope glycoprotein gp160, : 1 : 3 : 100 entities Detail

Interaction partners 1. Envelope glycoprotein gp160, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N Trosy HSQC

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 15N, 2H Envelope glycoprotein gp160, 50 mM DMPC, 100 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DMPC	natural abundance	50 mM
2	DHPC	natural abundance	100 mM
3	Envelope glycoprotein gp160	15N, 2H

2 3D HNCA

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 15N, 2H, 13C Envelope glycoprotein gp160, 50 mM DMPC, 100 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	DMPC	natural abundance	50 mM
5	DHPC	natural abundance	100 mM
6	Envelope glycoprotein gp160	[U-13C; U-15N; U-2H]

3 3D HN(CO)CA

Instrument

Bruker AvanceII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
4	DMPC	natural abundance	50 mM
5	DHPC	natural abundance	100 mM
6	Envelope glycoprotein gp160	[U-13C; U-15N; U-2H]

4 3D HNCO

Instrument

Bruker AvanceII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
4	DMPC	natural abundance	50 mM
5	DHPC	natural abundance	100 mM
6	Envelope glycoprotein gp160	[U-13C; U-15N; U-2H]

5 3D 1H-15N NOESY tr-HSQC

Instrument

Bruker AvanceIII - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 15N, 13C Envelope glycoprotein gp160, 50 mM [U-99% 2H] DMPC, 100 mM [U-99% 2H] DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	DMPC	[U-99% 2H]	50 mM
8	DHPC	[U-99% 2H]	100 mM
9	Envelope glycoprotein gp160	[U-100% 13C; U-100% 15N]

6 3D Jch Modulated 1H-15N NOESY

Instrument

Bruker AvanceII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 15N, 2H mixed with 13C Envelope glycoprotein gp160, 50 mM [U-99% 2H] DMPC, 100 mM [U-99% 2H] DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	DMPC	[U-99% 2H]	50 mM
14	DHPC	[U-99% 2H]	100 mM
15	Envelope glycoprotein gp160	15N, 2H mixed with 13C

7 3D 1H-13C NOESY

Instrument

Bruker AvanceII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 15N, 2H mixed with 13C(15%) Envelope glycoprotein gp160, 50 mM [U-99% 2H] DMPC, 100 mM [U-99% 2H] DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
10	DMPC	[U-99% 2H]	50 mM
11	DHPC	[U-99% 2H]	100 mM
12	Envelope glycoprotein gp160	15N, 2H mixed with 13C(15%)

8 3D 1H-15N NOESY tr-HSQC

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
10	DMPC	[U-99% 2H]	50 mM
11	DHPC	[U-99% 2H]	100 mM
12	Envelope glycoprotein gp160	15N, 2H mixed with 13C(15%)

9 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
7	DMPC	[U-99% 2H]	50 mM
8	DHPC	[U-99% 2H]	100 mM
9	Envelope glycoprotein gp160	[U-100% 13C; U-100% 15N]

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30503_6e8w.nef
Input source #2: Coordindates	6e8w.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

660-----670-------680-------690-------700-------710
LLELDKWASLWNWFDITNWLWYIRIFIIIVGSLIGLRIVFAVLSLVNRVRQ
|||||||||||||||||||||||||||||||||||||||||||||||||||
LLELDKWASLWNWFDITNWLWYIRIFIIIVGSLIGLRIVFAVLSLVNRVRQ
--------10--------20--------30--------40--------50-

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

660-----670-------680-------690-------700-------710
LLELDKWASLWNWFDITNWLWYIRIFIIIVGSLIGLRIVFAVLSLVNRVRQ
|||||||||||||||||||||||||||||||||||||||||||||||||||
LLELDKWASLWNWFDITNWLWYIRIFIIIVGSLIGLRIVFAVLSLVNRVRQ
--------10--------20--------30--------40--------50-

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

660-----670-------680-------690-------700-------710
LLELDKWASLWNWFDITNWLWYIRIFIIIVGSLIGLRIVFAVLSLVNRVRQ
|||||||||||||||||||||||||||||||||||||||||||||||||||
LLELDKWASLWNWFDITNWLWYIRIFIIIVGSLIGLRIVFAVLSLVNRVRQ
--------10--------20--------30--------40--------50-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	51	100.0
B	B	51	100.0
C	C	51	100.0

Content subtype: combined_30503_6e8w.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	188		98.0 (chain: A, length: 51)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	837 (1)	noe	98.0 (chain: A, length: 51), 98.0 (chain: B, length: 51), 98.0 (chain: C, length: 51)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	234 (234)	.	88.2 (chain: A, length: 51), 88.2 (chain: B, length: 51), 88.2 (chain: C, length: 51)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 51, Sequence coverage: 98.0%
- Total number of assignments
  - ¹H chemical shifts: 49
  - ¹³C chemical shifts: 90
  - ¹⁵N chemical shifts: 49
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	343	49	14.3
¹³C chemical shifts	270	90	33.3
¹⁵N chemical shifts	64	49	76.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	104	49	47.1
¹³C chemical shifts	102	90	88.2
¹⁵N chemical shifts	51	49	96.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	239	0	0.0
¹³C chemical shifts	168	0	0.0
¹⁵N chemical shifts	13	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	0	0.0
¹³C chemical shifts	47	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	0	0.0
¹³C chemical shifts	44	0	0.0
¹⁵N chemical shifts	5	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 51, Sequence coverage: 98.0%
  - Entity_assembly_ID: B, Chain length: 51, Sequence coverage: 98.0%
  - Entity_assembly_ID: C, Chain length: 51, Sequence coverage: 98.0%
- Total number of restraints: 837
- Weight of restraints: 1.0 (837)
- Potential type of restraints: square-well-parabolic (837)
- Range of distance target values: 1.95, 5.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 51, Sequence coverage: 88.2%
  - Entity_assembly_ID: B, Chain length: 51, Sequence coverage: 88.2%
  - Entity_assembly_ID: C, Chain length: 51, Sequence coverage: 88.2%
- Total number of restraints: 234
- Total number of restraints per polymer type: 234
- Weight of restraints: 1.0 (234)
- Potential type of restraints: square-well-parabolic (234)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C

Keywords MPER-TMD HIV-1 Env gp41, VIRAL PROTEIN

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Found 1 Document (0.551 seconds)

BMRB: 30503

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Related entities 1. Envelope glycoprotein gp160, : 1 : 3 : 100 entities Detail

Interaction partners 1. Envelope glycoprotein gp160, : 1 interactors Detail

Experiments performed 9 experiments Detail

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NMR combined restraints 4 contents Detail