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BMRB: 19764

2MK9

Spatial structure of the dimeric transmembrane domain of Toll-like receptor 3

Authors

Mineev, K.S., Goncharuk, S.A., Arseniev, A.S.

Assembly

dimeric transmembrane domain of Toll-like receptor 3

Entity

1. dimeric transmembrane domain of Toll-like receptor 3 (polymer, Thiol state: not present), 34 monomers, 4087.928 × 2 Da Detail

MDSAPFELFF MINTSILLIF IFIVLLIHFE GWRI

Total weight

8175.856 Da

Max. entity weight

4087.928 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.6 %, Completeness (bb): 98.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.6 % (422 of 451)	96.5 % (221 of 229)	89.8 % (168 of 187)	94.3 % (33 of 35)
Backbone	98.5 % (199 of 202)	100.0 % (68 of 68)	97.0 % (98 of 101)	100.0 % (33 of 33)
Sidechain	90.8 % (256 of 282)	95.0 % (153 of 161)	86.6 % (103 of 119)	0.0 % (0 of 2)
Aromatic	68.4 % (52 of 76)	81.6 % (31 of 38)	56.8 % (21 of 37)	0.0 % (0 of 1)
Methyl	100.0 % (56 of 56)	100.0 % (28 of 28)	100.0 % (28 of 28)

1. entity

MDSAPFELFF MINTSILLIF IFIVLLIHFE GWRI

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	natural abundance		0.8 mM
2	entity	[U-98% 13C; U-98% 15N]		1.2 mM
3	potassium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	DPC	[U-99% 2H]		200 mM
6	H2O	natural abundance
7	D2O	natural abundance		5 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2MK9, Strand ID: A, B Detail

Release date

2014-09-14

Citation

Toll-like receptor 3 transmembrane domain is able to perform various homotypic interactions: an NMR structural study
Mineev, K., Goncharuk, S., Arseniev, A.
FEBS Lett. (2014), 588, 3802-3807, PubMed 25217833 , DOI 10.1016/j.febslet.2014.08.031 , Abstract

Related entities 1. dimeric transmembrane domain of Toll-like receptor 3, : 1 : 1 : 2 : 8 entities Detail

Interaction partners 1. dimeric transmembrane domain of Toll-like receptor 3, : 14 interactors Detail

More details for 14 interactors identified by 8 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	natural abundance		0.8 mM
2	entity	[U-98% 13C; U-98% 15N]		1.2 mM
3	potassium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	DPC	[U-99% 2H]		200 mM
6	H2O	natural abundance
7	D2O	natural abundance		5 %

2 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	natural abundance		0.8 mM
2	entity	[U-98% 13C; U-98% 15N]		1.2 mM
3	potassium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	DPC	[U-99% 2H]		200 mM
6	H2O	natural abundance
7	D2O	natural abundance		5 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	natural abundance		0.8 mM
2	entity	[U-98% 13C; U-98% 15N]		1.2 mM
3	potassium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	DPC	[U-99% 2H]		200 mM
6	H2O	natural abundance
7	D2O	natural abundance		5 %

4 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	natural abundance		0.8 mM
2	entity	[U-98% 13C; U-98% 15N]		1.2 mM
3	potassium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	DPC	[U-99% 2H]		200 mM
6	H2O	natural abundance
7	D2O	natural abundance		5 %

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	natural abundance		0.8 mM
2	entity	[U-98% 13C; U-98% 15N]		1.2 mM
3	potassium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	DPC	[U-99% 2H]		200 mM
6	H2O	natural abundance
7	D2O	natural abundance		5 %

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	natural abundance		0.8 mM
2	entity	[U-98% 13C; U-98% 15N]		1.2 mM
3	potassium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	DPC	[U-99% 2H]		200 mM
6	H2O	natural abundance
7	D2O	natural abundance		5 %

7 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	natural abundance		0.8 mM
2	entity	[U-98% 13C; U-98% 15N]		1.2 mM
3	potassium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	DPC	[U-99% 2H]		200 mM
6	H2O	natural abundance
7	D2O	natural abundance		5 %

8 3D HCCH-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	natural abundance		0.8 mM
2	entity	[U-98% 13C; U-98% 15N]		1.2 mM
3	potassium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	DPC	[U-99% 2H]		200 mM
6	H2O	natural abundance
7	D2O	natural abundance		5 %

9 13C/15N-filtered NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	natural abundance		0.8 mM
2	entity	[U-98% 13C; U-98% 15N]		1.2 mM
3	potassium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		1 mM
5	DPC	[U-99% 2H]		200 mM
6	H2O	natural abundance
7	D2O	natural abundance		5 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19764_2mk9.nef
Input source #2: Coordindates	2mk9.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----
MDSAPFELFFMINTSILLIFIFIVLLIHFEGWRI
||||||||||||||||||||||||||||||||||
MDSAPFELFFMINTSILLIFIFIVLLIHFEGWRI

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

-------110-------120-------130----
MDSAPFELFFMINTSILLIFIFIVLLIHFEGWRI
||||||||||||||||||||||||||||||||||
MDSAPFELFFMINTSILLIFIFIVLLIHFEGWRI
--------10--------20--------30----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	34	0	0	100.0
B	B	34	0	0	100.0

Content subtype: combined_19764_2mk9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	426		100.0 (chain: A, length: 34)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	563 (1)	noe	100.0 (chain: A, length: 34), 100.0 (chain: B, length: 34)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	801 (1)	noe	100.0 (chain: A, length: 34), 100.0 (chain: B, length: 34)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	136 (136)	.	91.2 (chain: A, length: 34), 91.2 (chain: B, length: 34)
2	Dihedral angle restraints	DYANA/DIANA_dihedral_5	OK	204 (204)	.	91.2 (chain: A, length: 34), 91.2 (chain: B, length: 34)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 224
  - ¹³C chemical shifts: 168
  - ¹⁵N chemical shifts: 34
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 34, Sequence coverage: 100.0%
- Total number of restraints: 561
- Weight of restraints: 1.0 (561)
- Potential type of restraints: upper-bound-parabolic (561)
- Range of distance target values: 0.0, 5.07 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 100.0%
    - Entity_assembly_ID: B, Chain length: 34, Sequence coverage: 100.0%
  - Total number of restraints: 764
  - Weight of restraints: 1.0 (764)
  - Potential type of restraints: upper-bound-parabolic (764)
  - Range of distance target values: 0.0, 5.07 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - 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: 34, Sequence coverage: 91.2%
  - Entity_assembly_ID: B, Chain length: 34, Sequence coverage: 91.2%
- Total number of restraints: 136
- Total number of restraints per polymer type: 136
- Weight of restraints: 1.0 (136)
- Potential type of restraints: square-well-parabolic (136)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Saveframe: DYANA/DIANA_dihedral_5
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 91.2%
    - Entity_assembly_ID: B, Chain length: 34, Sequence coverage: 91.2%
  - Total number of restraints: 204
  - Total number of restraints per polymer type: 204
  - Weight of restraints: 1.0 (204)
  - Potential type of restraints: square-well-parabolic (204)
  - Plot of Phi-Psi angle restraints
  - Plot of Chi1-Chi2 angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A
    - Chain_ID: B

Keywords dimer, Toll-like receptor, transmembrane, transmembrane domain