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BMRB: 19673

2MIC

NMR structure of p75 transmembrane domain in DPC micelles

Authors

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

Assembly

p75 transmembrane domain

Entity

1. p75 transmembrane domain (polymer), 41 monomers, 4557.298 × 2 Da Detail

MTRGTTDNLI PVYCSILAAV VVGLVAYIAF KRWNSSKQNK Q

Total weight

9114.596 Da

Max. entity weight

4557.298 Da

Source organism

Rattus norvegicus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.6 %, Completeness: 89.0 %, Completeness (bb): 91.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.0 % (430 of 483)	90.3 % (224 of 248)	87.3 % (165 of 189)	89.1 % (41 of 46)
Backbone	91.8 % (224 of 244)	92.8 % (77 of 83)	89.3 % (108 of 121)	97.5 % (39 of 40)
Sidechain	87.1 % (242 of 278)	89.1 % (147 of 165)	86.9 % (93 of 107)	33.3 % (2 of 6)
Aromatic	78.9 % (30 of 38)	94.7 % (18 of 19)	66.7 % (12 of 18)	0.0 % (0 of 1)
Methyl	93.1 % (54 of 58)	93.1 % (27 of 29)	93.1 % (27 of 29)

1. p75-TM-wt

MTRGTTDNLI PVYCSILAAV VVGLVAYIAF KRWNSSKQNK Q

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	p75-TM-wt	[U-100% 13C; U-100% 15N]		1.9 mM
2	DPC	[U-98% 2H]		95 mM
3	sodium phosphate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

Protein Blocks Logo

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

Release date

2014-12-21

Citation

Structure of dimeric p75 neurotrophin receptor transmembrane domain provides insight on neurotrophin signaling
Nadezhdin, K., Arseniev, A., Goncharuk, S., Mineev, K., Vilar, M.
Not known

Related entities 1. p75 transmembrane domain, : 1 : 2 : 18 entities Detail

Interaction partners 1. p75 transmembrane domain, : 19 interactors Detail

More details for 19 interactors identified by 9 citations

Experiments performed 10 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	p75-TM-wt	[U-100% 13C; U-100% 15N]		1.9 mM
2	DPC	[U-98% 2H]		95 mM
3	sodium phosphate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

2 2D 1H-13C HSQC aliphatic

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	p75-TM-wt	[U-100% 13C; U-100% 15N]		1.9 mM
2	DPC	[U-98% 2H]		95 mM
3	sodium phosphate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

3 2D 1H-13C HSQC aromatic

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	p75-TM-wt	[U-100% 13C; U-100% 15N]		1.9 mM
2	DPC	[U-98% 2H]		95 mM
3	sodium phosphate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

4 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	p75-TM-wt	[U-100% 13C; U-100% 15N]		1.9 mM
2	DPC	[U-98% 2H]		95 mM
3	sodium phosphate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

5 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	p75-TM-wt	[U-100% 13C; U-100% 15N]		1.9 mM
2	DPC	[U-98% 2H]		95 mM
3	sodium phosphate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

6 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	p75-TM-wt	[U-100% 13C; U-100% 15N]		1.9 mM
2	DPC	[U-98% 2H]		95 mM
3	sodium phosphate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	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	p75-TM-wt	[U-100% 13C; U-100% 15N]		1.9 mM
2	DPC	[U-98% 2H]		95 mM
3	sodium phosphate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

8 3D 1H-15N TOCSY

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	p75-TM-wt	[U-100% 13C; U-100% 15N]		1.9 mM
2	DPC	[U-98% 2H]		95 mM
3	sodium phosphate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

9 3D 1H-13C NOESY aliphatic

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	p75-TM-wt	[U-100% 13C; U-100% 15N]		1.9 mM
2	DPC	[U-98% 2H]		95 mM
3	sodium phosphate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

10 3D 15N- and 13C-edited NOESY and 15N,13C-F1-filtered/F3-edited-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	p75-TM-wt	[U-100% 13C; U-100% 15N]		1.9 mM
2	DPC	[U-98% 2H]		95 mM
3	sodium phosphate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	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_19673_2mic.nef
Input source #2: Coordindates	2mic.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:14:CYS:SG	B:114:CYS:SG	oxidized, CA 59.085, CB 41.529 ppm	unknown	1.899

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-
MTRGTTDNLIPVYCSILAAVVVGLVAYIAFKRWNSSKQNKQ
|||||||||||||||||||||||||||||||||||||||||
MTRGTTDNLIPVYCSILAAVVVGLVAYIAFKRWNSSKQNKQ

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

-------110-------120-------130-------140-
MTRGTTDNLIPVYCSILAAVVVGLVAYIAFKRWNSSKQNKQ
|||||||||||||||||||||||||||||||||||||||||
MTRGTTDNLIPVYCSILAAVVVGLVAYIAFKRWNSSKQNKQ
--------10--------20--------30--------40-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	41	0	0	100.0
B	B	41	0	0	100.0

Content subtype: combined_19673_2mic.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	445		97.6 (chain: A, length: 41)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	236 (1)	noe	95.1 (chain: A, length: 41)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	6 (1)	undefined	No information
3	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	84 (1)	hbond	43.9 (chain: A, length: 41)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_5	OK	93 (93)	.	61.0 (chain: A, length: 41), 48.8 (chain: B, length: 41)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 97.6%
- Total number of assignments
  - ¹H chemical shifts: 233
  - ¹³C chemical shifts: 170
  - ¹⁵N chemical shifts: 42
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 95.1%
- Total number of restraints: 235
- Weight of restraints: 1.0 (235)
- Potential type of restraints: upper-bound-parabolic (235)
- Range of distance target values: 2.4, 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: Warning
  - Experiment type: undefined
  - Total number of restraints: 6
  - Weight of restraints: 1.0 (6)
  - Potential type of restraints: upper-bound-parabolic (6)
  - Range of distance target values: 2.0, 3.1 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in 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: 41, Sequence coverage: 43.9%
    - Total number of restraints: 84
    - Weight of restraints: 1.0 (84)
    - Potential type of restraints: upper-bound-parabolic (84)
    - 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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 61.0%
  - Entity_assembly_ID: B, Chain length: 41, Sequence coverage: 48.8%
- Total number of restraints: 93
- Total number of restraints per polymer type: 93
- Weight of restraints: 1.0 (93)
- Potential type of restraints: square-well-parabolic (93)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords dimer, p75, protein, transmembrane