BMRBj - BMREntryMaster

Found 1 Document (0.67 seconds)

BMRB: 30678

6UJU

Structure of the HIV-1 gp41 transmembrane domain and cytoplasmic tail (LLP2)

Authors

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

Assembly

Envelope glycoprotein GP41

Entity

1. Envelope glycoprotein GP41 (polymer, Thiol state: not present), 112 monomers, 13021.02 × 3 Da Detail

NWLWYIRIFI IIVGSLIGLR IVFAVLSLVN RVRQGYSPLS FQTHLPTPRG PDRPEGIEEE GGERDRDRSI RLVNGSLALI WDDLRSLSLF SYHRLRDLLL IVTRIVELLG RR

Total weight

39063.06 Da

Max. entity weight

13021.02 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: 96.4 %, Completeness: 36.0 %, Completeness (bb): 71.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	36.0 % (493 of 1368)	16.8 % (120 of 713)	50.6 % (273 of 540)	87.0 % (100 of 115)
Backbone	71.3 % (472 of 662)	46.1 % (105 of 228)	81.7 % (267 of 327)	93.5 % (100 of 107)
Sidechain	9.9 % (80 of 809)	3.1 % (15 of 485)	20.6 % (65 of 316)	0.0 % (0 of 8)
Aromatic	0.0 % (0 of 108)	0.0 % (0 of 54)	0.0 % (0 of 51)	0.0 % (0 of 3)
Methyl	3.0 % (5 of 166)	2.4 % (2 of 83)	3.6 % (3 of 83)

1. entity 1

NWLWYIRIFI IIVGSLIGLR IVFAVLSLVN RVRQGYSPLS FQTHLPTPRG PDRPEGIEEE GGERDRDRSI RLVNGSLALI WDDLRSLSLF SYHRLRDLLL IVTRIVELLG RR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 0.7 mM [U-13C; U-15N; U-85% 2H] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 40 mM DMPC, 80 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HIV-1 gp41 TMD-CT(LLP2)	[U-13C; U-15N; U-85% 2H]	0.7 mM
2	MES	natural abundance	40 mM
3	DMPC	natural abundance	40 mM
4	DHPC	natural abundance	80 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 0.8 mM [U-15N; U-2H] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 40 mM DMPC, 80 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
5	HIV-1 gp41 TMD-CT(LLP2)	[U-15N; U-2H]	0.8 mM
6	MES	natural abundance	40 mM
7	DMPC	natural abundance	40 mM
8	DHPC	natural abundance	80 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 1.0 mM [U-13C; U-15N] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 40 mM DMPC, 80 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
9	HIV-1 gp41 TMD-CT(LLP2)	[U-13C; U-15N]	1.0 mM
10	MES	natural abundance	40 mM
11	DMPC	natural abundance	40 mM
12	DHPC	natural abundance	80 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 0.5 mM [U-15N; U-2H] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 40 mM DMPC, 80 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	HIV-1 gp41 TMD-CT(LLP2)	[U-15N; U-2H]	0.5 mM
14	MES	natural abundance	40 mM
15	DMPC	natural abundance	40 mM
16	DHPC	natural abundance	80 mM

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 0.5 mM [U-15N; U-2H] HIV-1 gp41 TMD-CT (LLP2), 0.5 mM [U-13C] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 40 mM DMPC, 80 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
17	HIV-1 gp41 TMD-CT(LLP2)	[U-13C]	0.5 mM
18	MES	natural abundance	40 mM
19	DMPC	natural abundance	40 mM
20	DHPC	natural abundance	80 mM
21	HIV-1 gp41 TMD-CT (LLP2)	[U-15N; U-2H]	0.5 mM

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 0.5 mM [U-15N; U-85% 2H] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 40 mM DMPC, 80 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
22	HIV-1 gp41 TMD-CT(LLP2)	[U-15N; U-85% 2H]	0.5 mM
23	MES	natural abundance	40 mM
24	DMPC	natural abundance	40 mM
25	DHPC	natural abundance	80 mM

Protein Blocks Logo

Calculated from 15 models in PDB: 6UJU, Strand ID: A, B, C Detail

Release date

2019-10-08

Citation

Structural basis of transmembrane coupling of the HIV-1 envelope glycoprotein
Piai, A., Fu, Q., Cai, Y., Ghantous, F., Xiao, T., Shaik, M.M., Peng, H., Rits-Volloch, S., Chen, W., Seaman, M.S., Chen, B., Chou, J.J.
Nat. Commun. (2020), 11, 2317-2317, PubMed 32385256 , DOI 10.1038/s41467-020-16165-0 , Abstract

Related entities 1. Envelope glycoprotein GP41, : 1 : 1 : 60 entities Detail

Interaction partners 1. Envelope glycoprotein GP41, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 22 experiments Detail

1 2D 1H-15N TROSY-HSQC

Instrument

Bruker AVANCE III HD - 600 MHz Equipped with a cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 0.7 mM [U-13C; U-15N; U-85% 2H] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 40 mM DMPC, 80 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HIV-1 gp41 TMD-CT(LLP2)	[U-13C; U-15N; U-85% 2H]	0.7 mM
2	MES	natural abundance	40 mM
3	DMPC	natural abundance	40 mM
4	DHPC	natural abundance	80 mM

2 3D TROSY HNCO

Instrument

Bruker AVANCE III HD - 600 MHz Equipped with a cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
1	HIV-1 gp41 TMD-CT(LLP2)	[U-13C; U-15N; U-85% 2H]	0.7 mM
2	MES	natural abundance	40 mM
3	DMPC	natural abundance	40 mM
4	DHPC	natural abundance	80 mM

3 3D TROSY HNCA

Instrument

Bruker AVANCE III HD - 600 MHz Equipped with a cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
1	HIV-1 gp41 TMD-CT(LLP2)	[U-13C; U-15N; U-85% 2H]	0.7 mM
2	MES	natural abundance	40 mM
3	DMPC	natural abundance	40 mM
4	DHPC	natural abundance	80 mM

4 2D 1H-15N TROSY-HSQC

Instrument

Bruker AVANCE III - 750 MHz Equipped with a cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
1	HIV-1 gp41 TMD-CT(LLP2)	[U-13C; U-15N; U-85% 2H]	0.7 mM
2	MES	natural abundance	40 mM
3	DMPC	natural abundance	40 mM
4	DHPC	natural abundance	80 mM

5 3D TROSY HN(CA)CO

Instrument

Bruker AVANCE III - 750 MHz Equipped with a cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
1	HIV-1 gp41 TMD-CT(LLP2)	[U-13C; U-15N; U-85% 2H]	0.7 mM
2	MES	natural abundance	40 mM
3	DMPC	natural abundance	40 mM
4	DHPC	natural abundance	80 mM

6 3D TROSY HN(CO)CA

Instrument

Bruker AVANCE III - 750 MHz Equipped with a cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
1	HIV-1 gp41 TMD-CT(LLP2)	[U-13C; U-15N; U-85% 2H]	0.7 mM
2	MES	natural abundance	40 mM
3	DMPC	natural abundance	40 mM
4	DHPC	natural abundance	80 mM

7 3D TROSY HNCACB

Instrument

Bruker AVANCE III - 750 MHz Equipped with a cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
1	HIV-1 gp41 TMD-CT(LLP2)	[U-13C; U-15N; U-85% 2H]	0.7 mM
2	MES	natural abundance	40 mM
3	DMPC	natural abundance	40 mM
4	DHPC	natural abundance	80 mM

8 2D 1H-15N TROSY-HSQC

Instrument

Bruker AVANCE III - 750 MHz Equipped with a cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 0.8 mM [U-15N; U-2H] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 40 mM DMPC, 80 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
5	HIV-1 gp41 TMD-CT(LLP2)	[U-15N; U-2H]	0.8 mM
6	MES	natural abundance	40 mM
7	DMPC	natural abundance	40 mM
8	DHPC	natural abundance	80 mM

9 3D 15N-edited NOESY-TROSY-HSQC

Instrument

Bruker AVANCE III - 750 MHz Equipped with a cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
5	HIV-1 gp41 TMD-CT(LLP2)	[U-15N; U-2H]	0.8 mM
6	MES	natural abundance	40 mM
7	DMPC	natural abundance	40 mM
8	DHPC	natural abundance	80 mM

10 2D 1H-15N TROSY-HSQC

Instrument

Bruker AVANCE III - 800 MHz Equipped with a cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 1.0 mM [U-13C; U-15N] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 40 mM DMPC, 80 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
9	HIV-1 gp41 TMD-CT(LLP2)	[U-13C; U-15N]	1.0 mM
10	MES	natural abundance	40 mM
11	DMPC	natural abundance	40 mM
12	DHPC	natural abundance	80 mM

11 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - 800 MHz Equipped with a cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
9	HIV-1 gp41 TMD-CT(LLP2)	[U-13C; U-15N]	1.0 mM
10	MES	natural abundance	40 mM
11	DMPC	natural abundance	40 mM
12	DHPC	natural abundance	80 mM

12 3D 15N-edited NOESY-TROSY-HSQC

Instrument

Bruker AVANCE III - 800 MHz Equipped with a cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
9	HIV-1 gp41 TMD-CT(LLP2)	[U-13C; U-15N]	1.0 mM
10	MES	natural abundance	40 mM
11	DMPC	natural abundance	40 mM
12	DHPC	natural abundance	80 mM

13 3D 13C-edited NOESY

Instrument

Bruker AVANCE III - 800 MHz Equipped with a cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
9	HIV-1 gp41 TMD-CT(LLP2)	[U-13C; U-15N]	1.0 mM
10	MES	natural abundance	40 mM
11	DMPC	natural abundance	40 mM
12	DHPC	natural abundance	80 mM

14 2D 1H-15N TROSY-HSQC

Instrument

Bruker AVANCE III - 900 MHz Equipped with a cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 0.5 mM [U-15N; U-2H] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 40 mM DMPC, 80 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	HIV-1 gp41 TMD-CT(LLP2)	[U-15N; U-2H]	0.5 mM
14	MES	natural abundance	40 mM
15	DMPC	natural abundance	40 mM
16	DHPC	natural abundance	80 mM

15 3D 15N-edited NOESY-TROSY-HSQC

Instrument

Bruker AVANCE III - 900 MHz Equipped with a cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
13	HIV-1 gp41 TMD-CT(LLP2)	[U-15N; U-2H]	0.5 mM
14	MES	natural abundance	40 mM
15	DMPC	natural abundance	40 mM
16	DHPC	natural abundance	80 mM

16 2D 1H-15N TROSY-HSQC

Instrument

Bruker AVANCE III - 900 MHz Equipped with a cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 0.5 mM [U-15N; U-2H] HIV-1 gp41 TMD-CT (LLP2), 0.5 mM [U-13C] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 40 mM DMPC, 80 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
17	HIV-1 gp41 TMD-CT(LLP2)	[U-13C]	0.5 mM
18	MES	natural abundance	40 mM
19	DMPC	natural abundance	40 mM
20	DHPC	natural abundance	80 mM
21	HIV-1 gp41 TMD-CT (LLP2)	[U-15N; U-2H]	0.5 mM

17 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - 900 MHz Equipped with a cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
17	HIV-1 gp41 TMD-CT(LLP2)	[U-13C]	0.5 mM
18	MES	natural abundance	40 mM
19	DMPC	natural abundance	40 mM
20	DHPC	natural abundance	80 mM
21	HIV-1 gp41 TMD-CT (LLP2)	[U-15N; U-2H]	0.5 mM

18 3D 15N-edited NOESY-TROSY-HSQC

Instrument

Bruker AVANCE III - 900 MHz Equipped with a cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
17	HIV-1 gp41 TMD-CT(LLP2)	[U-13C]	0.5 mM
18	MES	natural abundance	40 mM
19	DMPC	natural abundance	40 mM
20	DHPC	natural abundance	80 mM
21	HIV-1 gp41 TMD-CT (LLP2)	[U-15N; U-2H]	0.5 mM

19 2D 1H-15N TROSY-HSQC

Instrument

Bruker AVANCE III - 800 MHz Equipped with a cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
17	HIV-1 gp41 TMD-CT(LLP2)	[U-13C]	0.5 mM
18	MES	natural abundance	40 mM
19	DMPC	natural abundance	40 mM
20	DHPC	natural abundance	80 mM
21	HIV-1 gp41 TMD-CT (LLP2)	[U-15N; U-2H]	0.5 mM

20 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - 800 MHz Equipped with a cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
17	HIV-1 gp41 TMD-CT(LLP2)	[U-13C]	0.5 mM
18	MES	natural abundance	40 mM
19	DMPC	natural abundance	40 mM
20	DHPC	natural abundance	80 mM
21	HIV-1 gp41 TMD-CT (LLP2)	[U-15N; U-2H]	0.5 mM

21 3D J(CH)-modulated NOESY

Instrument

Bruker AVANCE III - 800 MHz Equipped with a cryogenic probe

Sample

#	Name	Isotope labeling	Concentration
17	HIV-1 gp41 TMD-CT(LLP2)	[U-13C]	0.5 mM
18	MES	natural abundance	40 mM
19	DMPC	natural abundance	40 mM
20	DHPC	natural abundance	80 mM
21	HIV-1 gp41 TMD-CT (LLP2)	[U-15N; U-2H]	0.5 mM

22 2D 1H-15N TROSY-HSQC

Instrument

Bruker AVANCE III HD - 600 MHz Equipped with a cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.7, Details 0.5 mM [U-15N; U-85% 2H] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 40 mM DMPC, 80 mM DHPC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
22	HIV-1 gp41 TMD-CT(LLP2)	[U-15N; U-85% 2H]	0.5 mM
23	MES	natural abundance	40 mM
24	DMPC	natural abundance	40 mM
25	DHPC	natural abundance	80 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30678_3.str
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	OK

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr30678_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	460		95.5 (chain: 1, length: 112)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 112, Sequence coverage: 95.5%
- Total number of assignments
  - ¹³C chemical shifts: 262
  - ¹H chemical shifts: 99
  - ¹⁵N chemical shifts: 99
- Completeness of assignments
  - Entity_assemble_ID: 1
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	540	262	48.5
¹H chemical shifts	713	99	13.9
¹⁵N chemical shifts	131	99	75.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	224	207	92.4
¹H chemical shifts	228	99	43.4
¹⁵N chemical shifts	107	99	92.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	316	55	17.4
¹H chemical shifts	485	0	0.0
¹⁵N chemical shifts	24	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	83	1	1.2
¹H chemical shifts	83	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	51	0	0.0
¹H chemical shifts	54	0	0.0
¹⁵N chemical shifts	3	0	0.0

Keywords Cytoplasmic tail, Lipid bilayer, MEMBRANE PROTEIN, Transmembrane domain, Viral protein

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Found 1 Document (0.67 seconds)

BMRB: 30678

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Related entities 1. Envelope glycoprotein GP41, : 1 : 1 : 60 entities Detail

Interaction partners 1. Envelope glycoprotein GP41, : 1 interactors Detail

Experiments performed 22 experiments Detail

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Chemical shift validation 3 contents Detail