BMRBj - BMREntryMaster

	Total	¹H	¹³C	¹⁵N
All	91.7 % (387 of 422)	91.9 % (194 of 211)	91.3 % (158 of 173)	92.1 % (35 of 38)
Backbone	96.2 % (202 of 210)	95.8 % (68 of 71)	96.2 % (100 of 104)	97.1 % (34 of 35)
Sidechain	89.0 % (219 of 246)	90.0 % (126 of 140)	89.3 % (92 of 103)	33.3 % (1 of 3)
Aromatic	70.0 % (28 of 40)	80.0 % (16 of 20)	60.0 % (12 of 20)
Methyl	100.0 % (66 of 66)	100.0 % (33 of 33)	100.0 % (33 of 33)

1. entity 1

MNITSQMNKT IIGVSVLSVL VVSVVAVLVY KFYFH

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0, Details 1.0 mM [U-100% 13C; U-100% 15N] TLR4-TM, 100 mM [U-99% 2H] DPC, 20 mM sodium phosphate, 0.01 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	TLR4-TM	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	DPC	[U-99% 2H]	100 (±1.0) mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	0.01 %

Protein Blocks Logo

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

Release date

2018-03-13

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, : 1 : 1 : 20 entities Detail

Experiments performed 5 experiments Detail

1 3D HNCO

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0, Details 1.0 mM [U-100% 13C; U-100% 15N] TLR4-TM, 100 mM [U-99% 2H] DPC, 20 mM sodium phosphate, 0.01 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	TLR4-TM	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	DPC	[U-99% 2H]	100 (±1.0) mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	0.01 %

2 3D HNCA

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TLR4-TM	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	DPC	[U-99% 2H]	100 (±1.0) mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	0.01 %

3 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TLR4-TM	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	DPC	[U-99% 2H]	100 (±1.0) mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	0.01 %

4 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TLR4-TM	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	DPC	[U-99% 2H]	100 (±1.0) mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	0.01 %

5 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TLR4-TM	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	DPC	[U-99% 2H]	100 (±1.0) mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	0.01 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34109_5nao.nef
Input source #2: Coordindates	5nao.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-----
MNITSQMNKTIIGVSVLSVLVVSVVAVLVYKFYFH
|||||||||||||||||||||||||||||||||||
MNITSQMNKTIIGVSVLSVLVVSVVAVLVYKFYFH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	35	0	0	100.0

Content subtype: combined_34109_5nao.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	384		100.0 (chain: A, length: 35)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	176 (1)	noe	100.0 (chain: A, length: 35)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	126 (1)	hbond	71.4 (chain: A, length: 35)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	63 (63)	.	80.0 (chain: A, length: 35)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 192
  - ¹³C chemical shifts: 158
  - ¹⁵N chemical shifts: 34
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	211	191	90.5
¹³C chemical shifts	173	158	91.3
¹⁵N chemical shifts	38	34	89.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	71	67	94.4
¹³C chemical shifts	70	66	94.3
¹⁵N chemical shifts	35	34	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	140	124	88.6
¹³C chemical shifts	103	92	89.3
¹⁵N chemical shifts	3	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	33	94.3
¹³C chemical shifts	35	33	94.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	16	80.0
¹³C chemical shifts	20	12	60.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 100.0%
- Total number of restraints: 176
- Weight of restraints: 1.0 (176)
- Potential type of restraints: upper-bound-parabolic (176)
- Range of distance target values: 2.4, 4.89 (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: 35, Sequence coverage: 71.4%
  - Total number of restraints: 126
  - Weight of restraints: 1.0 (126)
  - Potential type of restraints: upper-bound-parabolic (126)
  - 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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 80.0%
- Total number of restraints: 63
- Total number of restraints per polymer type: 63
- Weight of restraints: 1.0 (63)
- Potential type of restraints: square-well-parabolic (63)
- 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

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Found 1 Document (0.512 seconds)

BMRB: 34109

Sample

Related entities 1. Toll-like receptor 4, : 1 : 1 : 20 entities Detail

Experiments performed 5 experiments Detail

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Sample

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Sample

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NMR combined restraints 5 contents Detail