BMRBj - BMREntryMaster

Found 1 Document (0.757 seconds)

BMRB: 30090

5JYN

Structure of the transmembrane domain of HIV-1 gp41 in bicelle

Authors

Dev, J., Fu, Q., Park, D., Chen, B., Chou, J.J.

Assembly

Envelope glycoprotein gp160

Entity

1. Envelope glycoprotein gp160 (polymer, Thiol state: not present), 40 monomers, 4646.569 × 3 Da Detail

NWLWYIRIFI IIVGSLIGLR IVFAVLSLVN RVRQGYSPLS

Total weight

13939.707 Da

Max. entity weight

4646.569 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: 97.5 %, Completeness: 32.5 %, Completeness (bb): 64.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	32.5 % (166 of 510)	18.8 % (49 of 261)	39.0 % (80 of 205)	84.1 % (37 of 44)
Backbone	64.7 % (154 of 238)	48.8 % (40 of 82)	65.8 % (77 of 117)	94.9 % (37 of 39)
Sidechain	4.5 % (14 of 309)	5.0 % (9 of 179)	4.0 % (5 of 125)	0.0 % (0 of 5)
Aromatic	0.0 % (0 of 60)	0.0 % (0 of 30)	0.0 % (0 of 28)	0.0 % (0 of 2)
Methyl	5.4 % (4 of 74)	5.4 % (2 of 37)	5.4 % (2 of 37)

1. Envelope glycoprotein gp160

NWLWYIRIFI IIVGSLIGLR IVFAVLSLVN RVRQGYSPLS

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 6.7 (±0.1), Details 0.8 mM [U-13C; U-15N; 85%-2H] HIV-1 gp41 Transmembrane Domain, 60 mM regular 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 120 mM regular 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), 25 mM regular MES, 0.1 % regular NaN3, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)	natural abundance	120 (±3.0) mM
2	1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)	natural abundance	60 (±2.0) mM
3	HIV-1 gp41 Transmembrane Domain	[U-13C; U-15N; 85%-2H]	0.8 (±0.1) mM
4	MES	natural abundance	25 (±2.0) mM
5	NaN3	natural abundance	0.1 (±0.01) %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 6.7 (±0.1), Details 0.8 mM [U-13C; U-15N] HIV-1 gp41 Transmembrane Domain, 60 mM acyl chains 2H labeled 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 120 mM acyl chains 2H labeled 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), 25 mM regular MES, 0.1 % regular NaN3, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
6	1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)	acyl chains 2H labeled	120 (±3.0) mM
7	1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)	acyl chains 2H labeled	60 (±2.0) mM
8	HIV-1 gp41 Transmembrane Domain	[U-13C; U-15N]	0.8 (±0.1) mM
9	MES	natural abundance	25 (±2.0) mM
10	NaN3	natural abundance	0.1 (±0.01) %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 6.7 (±0.1), Details 0.4 mM [U-15N; U-2H] HIV-1 gp41 Transmembrane Domain, 0.4 mM [15% 13C] HIV-1 gp41 Transmembrane Domain, 60 mM acyl chains 2H labeled 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 120 mM acyl chains 2H labeled 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), 25 mM regular MES, 0.1 % regular NaN3, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
11	1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)	acyl chains 2H labeled	120 (±3.0) mM
12	1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)	acyl chains 2H labeled	60 (±2.0) mM
13	HIV-1 gp41 Transmembrane Domain	[U-15N; U-2H]	0.4 (±0.1) mM
14	HIV-1 gp41 Transmembrane Domain	[15% 13C]	0.4 (±0.1) mM
15	MES	natural abundance	25 (±2.0) mM
16	NaN3	natural abundance	0.1 (±0.01) %

Sample #4

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 6.7 (±0.1), Details 0.8 mM [U-15N] HIV-1 gp41 Transmembrane Domain, 60 mM acyl chains 2H labeled 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 120 mM acyl chains 2H labeled 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), 25 mM regular MES, 0.1 % regular NaN3, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
17	1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)	acyl chains 2H labeled	120 (±3.0) mM
18	1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)	acyl chains 2H labeled	60 (±2.0) mM
19	HIV-1 gp41 Transmembrane Domain	[U-15N]	0.8 (±0.1) mM
20	MES	natural abundance	25 (±2.0) mM
21	NaN3	natural abundance	0.1 (±0.01) %

Protein Blocks Logo

Calculated from 15 models in PDB: 5JYN, Strand ID: A, B, C Detail

Release date

2016-06-23

Citation

Structural basis for membrane anchoring of HIV-1 envelope spike
Dev, J., Park, D., Fu, Q., Chen, J., Ha, H.H., Ghantous, F., Herrmann, T., Chang, W., Liu, Z., Frey, G., Seaman, M.S., Chen, B., Chou, J.J.
Science (2016), 353, 172-175, PubMed 27338706 , DOI 10.1126/science.aaf7066 , Abstract

Related entities 1. Envelope glycoprotein gp160, : 1 : 1 : 78 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 3D TROSY HNCA

Instrument

Bruker AvanceII - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 6.7 (±0.1), Details 0.8 mM [U-13C; U-15N; 85%-2H] HIV-1 gp41 Transmembrane Domain, 60 mM regular 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 120 mM regular 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), 25 mM regular MES, 0.1 % regular NaN3, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)	natural abundance	120 (±3.0) mM
2	1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)	natural abundance	60 (±2.0) mM
3	HIV-1 gp41 Transmembrane Domain	[U-13C; U-15N; 85%-2H]	0.8 (±0.1) mM
4	MES	natural abundance	25 (±2.0) mM
5	NaN3	natural abundance	0.1 (±0.01) %

2 3D TROSY HNCOCA

Instrument

Bruker AvanceII - 600 MHz cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
1	1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)	natural abundance	120 (±3.0) mM
2	1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)	natural abundance	60 (±2.0) mM
3	HIV-1 gp41 Transmembrane Domain	[U-13C; U-15N; 85%-2H]	0.8 (±0.1) mM
4	MES	natural abundance	25 (±2.0) mM
5	NaN3	natural abundance	0.1 (±0.01) %

3 3D TROSY HNCACO

Instrument

Bruker AvanceII - 600 MHz cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
1	1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)	natural abundance	120 (±3.0) mM
2	1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)	natural abundance	60 (±2.0) mM
3	HIV-1 gp41 Transmembrane Domain	[U-13C; U-15N; 85%-2H]	0.8 (±0.1) mM
4	MES	natural abundance	25 (±2.0) mM
5	NaN3	natural abundance	0.1 (±0.01) %

4 3D TROSY HNCO

Instrument

Bruker AvanceII - 600 MHz cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
1	1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)	natural abundance	120 (±3.0) mM
2	1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)	natural abundance	60 (±2.0) mM
3	HIV-1 gp41 Transmembrane Domain	[U-13C; U-15N; 85%-2H]	0.8 (±0.1) mM
4	MES	natural abundance	25 (±2.0) mM
5	NaN3	natural abundance	0.1 (±0.01) %

5 3D 15N NOESY-TROSY-HSQC

Instrument

Bruker AvanceIII - 900 MHz cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 6.7 (±0.1), Details 0.8 mM [U-13C; U-15N] HIV-1 gp41 Transmembrane Domain, 60 mM acyl chains 2H labeled 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 120 mM acyl chains 2H labeled 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), 25 mM regular MES, 0.1 % regular NaN3, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
6	1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)	acyl chains 2H labeled	120 (±3.0) mM
7	1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)	acyl chains 2H labeled	60 (±2.0) mM
8	HIV-1 gp41 Transmembrane Domain	[U-13C; U-15N]	0.8 (±0.1) mM
9	MES	natural abundance	25 (±2.0) mM
10	NaN3	natural abundance	0.1 (±0.01) %

6 3D 13C NOESY-HSQC (Methyls)

Instrument

Bruker AvanceIII - 900 MHz cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
6	1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)	acyl chains 2H labeled	120 (±3.0) mM
7	1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)	acyl chains 2H labeled	60 (±2.0) mM
8	HIV-1 gp41 Transmembrane Domain	[U-13C; U-15N]	0.8 (±0.1) mM
9	MES	natural abundance	25 (±2.0) mM
10	NaN3	natural abundance	0.1 (±0.01) %

7 3D 15N NOESY-TROSY-HSQC (long mixing time)

Instrument

Bruker AvanceII - 750 MHz cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 6.7 (±0.1), Details 0.4 mM [U-15N; U-2H] HIV-1 gp41 Transmembrane Domain, 0.4 mM [15% 13C] HIV-1 gp41 Transmembrane Domain, 60 mM acyl chains 2H labeled 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 120 mM acyl chains 2H labeled 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), 25 mM regular MES, 0.1 % regular NaN3, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
11	1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)	acyl chains 2H labeled	120 (±3.0) mM
12	1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)	acyl chains 2H labeled	60 (±2.0) mM
13	HIV-1 gp41 Transmembrane Domain	[U-15N; U-2H]	0.4 (±0.1) mM
14	HIV-1 gp41 Transmembrane Domain	[15% 13C]	0.4 (±0.1) mM
15	MES	natural abundance	25 (±2.0) mM
16	NaN3	natural abundance	0.1 (±0.01) %

8 2D 15N TROSY-HSQC for GdDOTA titration

Instrument

Bruker AvanceII - 600 MHz cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
1	1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)	natural abundance	120 (±3.0) mM
2	1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)	natural abundance	60 (±2.0) mM
3	HIV-1 gp41 Transmembrane Domain	[U-13C; U-15N; 85%-2H]	0.8 (±0.1) mM
4	MES	natural abundance	25 (±2.0) mM
5	NaN3	natural abundance	0.1 (±0.01) %

9 3D 15N NOESY-TROSY-HSQC (short mixing time)

Instrument

Bruker AvanceII - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 6.7 (±0.1), Details 0.8 mM [U-15N] HIV-1 gp41 Transmembrane Domain, 60 mM acyl chains 2H labeled 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), 120 mM acyl chains 2H labeled 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), 25 mM regular MES, 0.1 % regular NaN3, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
17	1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC)	acyl chains 2H labeled	120 (±3.0) mM
18	1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC)	acyl chains 2H labeled	60 (±2.0) mM
19	HIV-1 gp41 Transmembrane Domain	[U-15N]	0.8 (±0.1) mM
20	MES	natural abundance	25 (±2.0) mM
21	NaN3	natural abundance	0.1 (±0.01) %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30090_5jyn.nef
Input source #2: Coordindates	5jyn.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

---680-----690-------700-------710------
NWLWYIRIFIIIVGSLIGLRIVFAVLSLVNRVRQGYSPLS
||||||||||||||||||||||||||||||||||||||||
NWLWYIRIFIIIVGSLIGLRIVFAVLSLVNRVRQGYSPLS
--------10--------20--------30--------40

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

---680-----690-------700-------710------
NWLWYIRIFIIIVGSLIGLRIVFAVLSLVNRVRQGYSPLS
||||||||||||||||||||||||||||||||||||||||
NWLWYIRIFIIIVGSLIGLRIVFAVLSLVNRVRQGYSPLS
--------10--------20--------30--------40

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

---680-----690-------700-------710------
NWLWYIRIFIIIVGSLIGLRIVFAVLSLVNRVRQGYSPLS
||||||||||||||||||||||||||||||||||||||||
NWLWYIRIFIIIVGSLIGLRIVFAVLSLVNRVRQGYSPLS
--------10--------20--------30--------40

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	40	100.0
B	B	40	100.0
C	C	40	100.0

Content subtype: combined_30090_5jyn.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	149		97.5 (chain: A, length: 40)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	732 (1)	noe	95.0 (chain: A, length: 40), 95.0 (chain: B, length: 40), 95.0 (chain: C, length: 40)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	210 (210)	.	95.0 (chain: A, length: 40), 95.0 (chain: B, length: 40), 95.0 (chain: C, length: 40)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 97.5%
- Total number of assignments
  - ¹³C chemical shifts: 75
  - ¹H chemical shifts: 37
  - ¹⁵N chemical shifts: 37
- 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 (%)
¹³C chemical shifts	205	75	36.6
¹H chemical shifts	261	37	14.2
¹⁵N chemical shifts	48	37	77.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	80	75	93.8
¹H chemical shifts	82	37	45.1
¹⁵N chemical shifts	39	37	94.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	125	0	0.0
¹H chemical shifts	179	0	0.0
¹⁵N chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	37	0	0.0
¹H chemical shifts	37	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	28	0	0.0
¹H chemical shifts	30	0	0.0
¹⁵N chemical shifts	2	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: 40, Sequence coverage: 95.0%
  - Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 95.0%
  - Entity_assembly_ID: C, Chain length: 40, Sequence coverage: 95.0%
- Total number of restraints: 732
- Weight of restraints: 1.0 (732)
- Potential type of restraints: square-well-parabolic (732)
- Range of distance target values: 2.2, 4.75 (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: 40, Sequence coverage: 95.0%
  - Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 95.0%
  - Entity_assembly_ID: C, Chain length: 40, Sequence coverage: 95.0%
- Total number of restraints: 210
- Total number of restraints per polymer type: 210
- Weight of restraints: 1.0 (210)
- Potential type of restraints: square-well-parabolic (210)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C

Keywords lipid bilayer, transmembrane domain, transmembrane trimer

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Found 1 Document (0.757 seconds)

BMRB: 30090

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. Envelope glycoprotein gp160, : 1 : 1 : 78 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