BMRBj - BMREntryMaster

	Total	¹H	¹³C	¹⁵N
All	95.3 % (545 of 572)	95.8 % (277 of 289)	94.0 % (218 of 232)	98.0 % (50 of 51)
Backbone	97.2 % (280 of 288)	95.0 % (95 of 100)	97.9 % (137 of 140)	100.0 % (48 of 48)
Sidechain	93.9 % (308 of 328)	96.3 % (182 of 189)	91.2 % (124 of 136)	66.7 % (2 of 3)
Aromatic	75.0 % (36 of 48)	95.8 % (23 of 24)	54.2 % (13 of 24)
Methyl	97.6 % (82 of 84)	95.2 % (40 of 42)	100.0 % (42 of 42)

1. entity 1

MNITSQMNKT IIGVSVLSVL VVSVVAVLVY KFYFHLMLLA GCIKYGRG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0 (±0.1), Details 0.5 mM [U-13C; U-15N] TLR4-TM, 71 mM DHPC, 29 mM DMPG, 10 mM imidazole, 0.01 % sodium azide, 90% H2O/10% D2O.

#	Name	Isotope labeling	Concentration
1	DHPC	natural abundance	71 (±1.0) mM
2	DMPG	natural abundance	29 (±1.0) mM
3	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
4	imidazole	natural abundance	10 mM
5	sodium azide	natural abundance	0.01 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0 (±0.1), Details 0.5 mM [U-13C; U-15N] TLR4-TM, 71 mM DHPC, 29 mM DMPC, 10 mM imidazole, 0.01 % sodium azide, 90% H2O/10% D2O.

#	Name	Isotope labeling	Concentration
6	DHPC	natural abundance	71 (±1.0) mM
7	DMPC	natural abundance	29 (±1.0) mM
8	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
9	imidazole	natural abundance	10 mM
10	sodium azide	natural abundance	0.01 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0 (±0.1), Details 0.5 mM [U-13C; U-15N] TLR4-TM, 50 mM [U-2H] DPC, 10 mM imidazole, 0.01 % sodium azide, 90% H2O/10% D2O.

#	Name	Isotope labeling	Concentration
11	DPC	[U-2H]	50 (±1.0) mM
12	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
13	imidazole	natural abundance	10 mM
14	sodium azide	natural abundance	0.01 %

Chem. Shift Complete2

Sequence coverage: 100.0 %, Completeness: 94.5 %, Completeness (bb): 97.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.5 % (1081 of 1144)	94.8 % (548 of 578)	93.8 % (435 of 464)	96.1 % (98 of 102)
Backbone	97.6 % (562 of 576)	95.0 % (190 of 200)	98.6 % (276 of 280)	100.0 % (96 of 96)
Sidechain	92.2 % (605 of 656)	94.7 % (358 of 378)	90.1 % (245 of 272)	33.3 % (2 of 6)
Aromatic	71.9 % (69 of 96)	93.8 % (45 of 48)	50.0 % (24 of 48)
Methyl	98.8 % (166 of 168)	97.6 % (82 of 84)	100.0 % (84 of 84)

1. entity 1

MNITSQMNKT IIGVSVLSVL VVSVVAVLVY KFYFHLMLLA GCIKYGRG

Show sample condition

Sample #1

#	Name	Isotope labeling	Concentration
1	DHPC	natural abundance	71 (±1.0) mM
2	DMPG	natural abundance	29 (±1.0) mM
3	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
4	imidazole	natural abundance	10 mM
5	sodium azide	natural abundance	0.01 %

Sample #2

#	Name	Isotope labeling	Concentration
6	DHPC	natural abundance	71 (±1.0) mM
7	DMPC	natural abundance	29 (±1.0) mM
8	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
9	imidazole	natural abundance	10 mM
10	sodium azide	natural abundance	0.01 %

Sample #3

#	Name	Isotope labeling	Concentration
11	DPC	[U-2H]	50 (±1.0) mM
12	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
13	imidazole	natural abundance	10 mM
14	sodium azide	natural abundance	0.01 %

Chem. Shift Complete3

Sequence coverage: 100.0 %, Completeness: 93.8 %, Completeness (bb): 97.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.8 % (1610 of 1716)	94.0 % (815 of 867)	93.2 % (649 of 696)	95.4 % (146 of 153)
Backbone	97.2 % (840 of 864)	94.7 % (284 of 300)	98.1 % (412 of 420)	100.0 % (144 of 144)
Sidechain	91.3 % (898 of 984)	93.7 % (531 of 567)	89.5 % (365 of 408)	22.2 % (2 of 9)
Aromatic	71.5 % (103 of 144)	93.1 % (67 of 72)	50.0 % (36 of 72)
Methyl	98.0 % (247 of 252)	96.8 % (122 of 126)	99.2 % (125 of 126)

1. entity 1

MNITSQMNKT IIGVSVLSVL VVSVVAVLVY KFYFHLMLLA GCIKYGRG

Show sample condition

Sample #1

#	Name	Isotope labeling	Concentration
1	DHPC	natural abundance	71 (±1.0) mM
2	DMPG	natural abundance	29 (±1.0) mM
3	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
4	imidazole	natural abundance	10 mM
5	sodium azide	natural abundance	0.01 %

Sample #2

#	Name	Isotope labeling	Concentration
6	DHPC	natural abundance	71 (±1.0) mM
7	DMPC	natural abundance	29 (±1.0) mM
8	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
9	imidazole	natural abundance	10 mM
10	sodium azide	natural abundance	0.01 %

Sample #3

#	Name	Isotope labeling	Concentration
11	DPC	[U-2H]	50 (±1.0) mM
12	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
13	imidazole	natural abundance	10 mM
14	sodium azide	natural abundance	0.01 %

Protein Blocks Logo

Calculated from 10 models in PDB: 5NAM, Strand ID: A Detail

Release date

2017-08-27

Citation

Spatial structure of TLR4 transmembrane domain in bicelles provides the insight into the receptor activation mechanism
Mineev, K.S., Goncharuk, S.A., Goncharuk, M.V., Volynsky, P.E., Novikova, E.V., Aresinev, A.S.
Sci. Rep. (2017), 7, 6864-6864, PubMed 28761155 , DOI 10.1038/s41598-017-07250-4 , Abstract

Related entities 1. Toll-like receptor 4, : 14 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0 (±0.1), Details 0.5 mM [U-13C; U-15N] TLR4-TM, 71 mM DHPC, 29 mM DMPG, 10 mM imidazole, 0.01 % sodium azide, 90% H2O/10% D2O.

#	Name	Isotope labeling	Concentration
1	DHPC	natural abundance	71 (±1.0) mM
2	DMPG	natural abundance	29 (±1.0) mM
3	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
4	imidazole	natural abundance	10 mM
5	sodium azide	natural abundance	0.01 %

2 3D HNCA

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DHPC	natural abundance	71 (±1.0) mM
2	DMPG	natural abundance	29 (±1.0) mM
3	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
4	imidazole	natural abundance	10 mM
5	sodium azide	natural abundance	0.01 %

3 3D HNCO

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DHPC	natural abundance	71 (±1.0) mM
2	DMPG	natural abundance	29 (±1.0) mM
3	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
4	imidazole	natural abundance	10 mM
5	sodium azide	natural abundance	0.01 %

4 3D HN(CO)CA

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DHPC	natural abundance	71 (±1.0) mM
2	DMPG	natural abundance	29 (±1.0) mM
3	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
4	imidazole	natural abundance	10 mM
5	sodium azide	natural abundance	0.01 %

5 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DHPC	natural abundance	71 (±1.0) mM
2	DMPG	natural abundance	29 (±1.0) mM
3	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
4	imidazole	natural abundance	10 mM
5	sodium azide	natural abundance	0.01 %

6 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DHPC	natural abundance	71 (±1.0) mM
2	DMPG	natural abundance	29 (±1.0) mM
3	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
4	imidazole	natural abundance	10 mM
5	sodium azide	natural abundance	0.01 %

7 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DHPC	natural abundance	71 (±1.0) mM
2	DMPG	natural abundance	29 (±1.0) mM
3	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
4	imidazole	natural abundance	10 mM
5	sodium azide	natural abundance	0.01 %

8 3D HCCH-COSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DHPC	natural abundance	71 (±1.0) mM
2	DMPG	natural abundance	29 (±1.0) mM
3	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
4	imidazole	natural abundance	10 mM
5	sodium azide	natural abundance	0.01 %

9 3D HN(CO)CA

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0 (±0.1), Details 0.5 mM [U-13C; U-15N] TLR4-TM, 71 mM DHPC, 29 mM DMPC, 10 mM imidazole, 0.01 % sodium azide, 90% H2O/10% D2O.

#	Name	Isotope labeling	Concentration
6	DHPC	natural abundance	71 (±1.0) mM
7	DMPC	natural abundance	29 (±1.0) mM
8	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
9	imidazole	natural abundance	10 mM
10	sodium azide	natural abundance	0.01 %

10 3D HNCA

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0 (±0.1), Details 0.5 mM [U-13C; U-15N] TLR4-TM, 71 mM DHPC, 29 mM DMPC, 10 mM imidazole, 0.01 % sodium azide, 90% H2O/10% D2O.

#	Name	Isotope labeling	Concentration
6	DHPC	natural abundance	71 (±1.0) mM
7	DMPC	natural abundance	29 (±1.0) mM
8	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
9	imidazole	natural abundance	10 mM
10	sodium azide	natural abundance	0.01 %

11 3D HN(CO)CA

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0 (±0.1), Details 0.5 mM [U-13C; U-15N] TLR4-TM, 50 mM [U-2H] DPC, 10 mM imidazole, 0.01 % sodium azide, 90% H2O/10% D2O.

#	Name	Isotope labeling	Concentration
11	DPC	[U-2H]	50 (±1.0) mM
12	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
13	imidazole	natural abundance	10 mM
14	sodium azide	natural abundance	0.01 %

12 3D HNCA

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
11	DPC	[U-2H]	50 (±1.0) mM
12	TLR4-TM	[U-13C; U-15N]	0.5 (±0.05) mM
13	imidazole	natural abundance	10 mM
14	sodium azide	natural abundance	0.01 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34108_5nam.nef
Input source #2: Coordindates	5nam.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--------40--------
MNITSQMNKTIIGVSVLSVLVVSVVAVLVYKFYFHLMLLAGCIKYGRG
||||||||||||||||||||||||||||||||||||||||||||||||
MNITSQMNKTIIGVSVLSVLVVSVVAVLVYKFYFHLMLLAGCIKYGRG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	48	0	0	100.0

Content subtype: combined_34108_5nam.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	551		100.0 (chain: A, length: 48)
2	Assigned chemical shifts	assigned_chemical_shifts_2	Warning	537		100.0 (chain: A, length: 48)
3	Assigned chemical shifts	assigned_chemical_shifts_3	Warning	542		100.0 (chain: A, length: 48)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	224 (1)	noe	97.9 (chain: A, length: 48)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	138 (1)	hbond	62.5 (chain: A, length: 48)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	87 (87)	.	77.1 (chain: A, length: 48)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 48, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 281
  - ¹³C chemical shifts: 221
  - ¹⁵N chemical shifts: 49
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Tautomeric state of HIS
- 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
Saveframe: assigned_chemical_shifts_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 48, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 272
  - ¹³C chemical shifts: 217
  - ¹⁵N chemical shifts: 48
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Tautomeric state of HIS
- 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
Saveframe: assigned_chemical_shifts_3
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 48, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 275
  - ¹³C chemical shifts: 219
  - ¹⁵N chemical shifts: 48
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Tautomeric state of HIS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
10	THR	HG1	1.001

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	289	279	96.5
¹³C chemical shifts	232	221	95.3
¹⁵N chemical shifts	52	49	94.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	100	96	96.0
¹³C chemical shifts	96	96	100.0
¹⁵N chemical shifts	48	48	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	189	183	96.8
¹³C chemical shifts	136	125	91.9
¹⁵N chemical shifts	4	1	25.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	45	100.0
¹³C chemical shifts	45	45	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	23	95.8
¹³C chemical shifts	24	13	54.2

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
10	THR	HG1	4.587

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	289	270	93.4
¹³C chemical shifts	232	217	93.5
¹⁵N chemical shifts	52	48	92.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	100	95	95.0
¹³C chemical shifts	96	96	100.0
¹⁵N chemical shifts	48	48	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	189	175	92.6
¹³C chemical shifts	136	121	89.0
¹⁵N chemical shifts	4	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	45	100.0
¹³C chemical shifts	45	45	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	22	91.7
¹³C chemical shifts	24	11	45.8

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
10	THR	HG1	4.587

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	289	273	94.5
¹³C chemical shifts	232	219	94.4
¹⁵N chemical shifts	52	48	92.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	100	95	95.0
¹³C chemical shifts	96	96	100.0
¹⁵N chemical shifts	48	48	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	189	178	94.2
¹³C chemical shifts	136	123	90.4
¹⁵N chemical shifts	4	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	45	100.0
¹³C chemical shifts	45	45	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	22	91.7
¹³C chemical shifts	24	12	50.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 48, Sequence coverage: 97.9%
- Total number of restraints: 224
- Weight of restraints: 1.0 (224)
- Potential type of restraints: upper-bound-parabolic (224)
- Range of distance target values: 0.0, 4.11 (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
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 48, Sequence coverage: 62.5%
  - Total number of restraints: 138
  - Weight of restraints: 1.0 (138)
  - Potential type of restraints: upper-bound-parabolic (138)
  - Range of distance target values: 1.7, 3.3 (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: 48, Sequence coverage: 77.1%
- Total number of restraints: 87
- Total number of restraints per polymer type: 87
- Weight of restraints: 1.0 (87)
- Potential type of restraints: square-well-parabolic (87)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PROTEIN, PROTEIN RECEPTOR, Toll-like receptor, signaling protein, transmembrane domain

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.555 seconds)

BMRB: 34108

Sample #1

Sample #2

Sample #3

Sample #1

Sample #2

Sample #3

Sample #1

Sample #2

Sample #3

Related entities 1. Toll-like receptor 4, : 14 entities Detail

Experiments performed 12 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail