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BMRB: 25872

2N90

TrkA transmembrane domain NMR structure in DPC micelles

Authors

Nadezhdin, K., Goncharuk, S., Arseniev, A.

Assembly

TrkA transmembrane domain

Entity

1. TrkA transmembrane domain (polymer), 39 monomers, 4208.042 × 2 Da Detail

MKKDETPFGV SVAVGLAVFA CLFLSTLLLV LNKAGRRNK

Total weight

8416.084 Da

Max. entity weight

4208.042 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 87.1 %, Completeness (bb): 91.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.1 % (400 of 459)	89.4 % (211 of 236)	82.5 % (151 of 183)	95.0 % (38 of 40)
Backbone	91.4 % (212 of 232)	95.0 % (76 of 80)	87.7 % (100 of 114)	94.7 % (36 of 38)
Sidechain	83.3 % (219 of 263)	86.5 % (135 of 156)	78.1 % (82 of 105)	100.0 % (2 of 2)
Aromatic	60.0 % (18 of 30)	100.0 % (15 of 15)	20.0 % (3 of 15)
Methyl	100.0 % (60 of 60)	100.0 % (30 of 30)	100.0 % (30 of 30)

1. entity

MKKDETPFGV SVAVGLAVFA CLFLSTLLLV LNKAGRRNK

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	entity	natural abundance		1 mM
3	DPC	[U-100% 2H]		40 mM
4	potassium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2N90, Strand ID: A, B Detail

Release date

2016-11-02

Citation

TrkA transmembrane domain NMR structure in DPC micelles
Nadezhdin, K., Goncharuk, S., Arseniev, A., Vilar, M.
Not known

Related entities 1. TrkA transmembrane domain, : 2 : 25 entities Detail

Interaction partners 1. TrkA transmembrane domain, : 14 interactors Detail

More details for 14 interactors identified by 10 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 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	entity	natural abundance		1 mM
3	DPC	[U-100% 2H]		40 mM
4	potassium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	entity	natural abundance		1 mM
3	DPC	[U-100% 2H]		40 mM
4	potassium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	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 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	entity	natural abundance		1 mM
3	DPC	[U-100% 2H]		40 mM
4	potassium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

4 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	entity	natural abundance		1 mM
3	DPC	[U-100% 2H]		40 mM
4	potassium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	entity	natural abundance		1 mM
3	DPC	[U-100% 2H]		40 mM
4	potassium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

6 3D HNHA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	entity	natural abundance		1 mM
3	DPC	[U-100% 2H]		40 mM
4	potassium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

7 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 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	entity	natural abundance		1 mM
3	DPC	[U-100% 2H]		40 mM
4	potassium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	entity	natural abundance		1 mM
3	DPC	[U-100% 2H]		40 mM
4	potassium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

9 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 5.9

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	entity	natural abundance		1 mM
3	DPC	[U-100% 2H]		40 mM
4	potassium phosphate	natural abundance		20 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25872_2n90.nef
Input source #2: Coordindates	2n90.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---------
MKKDETPFGVSVAVGLAVFACLFLSTLLLVLNKAGRRNK
|||||||||||||||||||||||||||||||||||||||
MKKDETPFGVSVAVGLAVFACLFLSTLLLVLNKAGRRNK

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

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	39	0	0	100.0
B	B	39	0	0	100.0

Content subtype: combined_25872_2n90.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	408		97.4 (chain: A, length: 39)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	191 (1)	noe	84.6 (chain: A, length: 39)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	111 (1)	noe	92.3 (chain: A, length: 39)
3	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	14 (1)	noe	17.9 (chain: A, length: 39), 15.4 (chain: B, length: 39)
4	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	125 (1)	hbond	64.1 (chain: A, length: 39)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 39, Sequence coverage: 97.4%
- Total number of assignments
  - ¹H chemical shifts: 217
  - ¹⁵N chemical shifts: 37
  - ¹³C chemical shifts: 154
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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: 39, Sequence coverage: 84.6%
- Total number of restraints: 191
- Weight of restraints: 1.0 (191)
- Potential type of restraints: upper-bound-parabolic (191)
- Range of distance target values: 2.6, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 39, Sequence coverage: 92.3%
  - Total number of restraints: 110
  - Weight of restraints: 1.0 (110)
  - Potential type of restraints: upper-bound-parabolic (110)
  - Range of distance target values: 2.53, 4.67 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_5
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 39, Sequence coverage: 17.9%
      - Entity_assembly_ID: B, Chain length: 39, Sequence coverage: 15.4%
    - Total number of restraints: 14
    - Weight of restraints: 1.0 (14)
    - Potential type of restraints: upper-bound-parabolic (14)
    - Range of distance target values: 2.7, 4.0 (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: Warning
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 39, Sequence coverage: 64.1%
        --------10--------20--------30--------- MKKDETPFGVSVAVGLAVFACLFLSTLLLVLNKAGRRNK ||||||||||||||||||||||||| .........VSVAVGLAVFACLFLSTLLLVLNKA --------10--------20--------30----
      - Total number of restraints: 125
        Medium range restraints, 1 < | i - j | < 5 : 42
        Backbone-backbone: 42
        Total hydrogen bond restraints: 83
        O...H-x: 21
        O...h-N: 20
        O...H-x (too close!): 21
        O...h-N (too close!): 21
      - Weight of restraints: 1.0 (125)
        Medium range restraints, 1 < | i - j | < 5 : 1.0 (42)
        Backbone-backbone: 1.0 (42)
        Total hydrogen bond restraints: 1.0 (83)
        O...H-x: 1.0 (21)
        O...h-N: 1.0 (20)
        O...H-x (too close!): 1.0 (21)
        O...h-N (too close!): 1.0 (21)
      - Potential type of restraints: upper-bound-parabolic (125)
        Medium range restraints, 1 < | i - j | < 5 : upper-bound-parabolic (42)
        Backbone-backbone: upper-bound-parabolic (42)
        Total hydrogen bond restraints: upper-bound-parabolic (83)
        O...H-x: upper-bound-parabolic (21)
        O...h-N: upper-bound-parabolic (20)
        O...H-x (too close!): upper-bound-parabolic (21)
        O...h-N (too close!): upper-bound-parabolic (21)
      - 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
        Chain_ID: B
        None
      - Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A

Keywords DPC micelles, NMR structure, neurotrophin receptor, transmembrane domain