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BMRB: 19741

2MJO

NMR structure of p75 transmembrane domain C257A mutant in DPC micelles

Authors

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

Assembly

p75-TM-C257A

Entity

1. p75-TM-C257A (polymer, Thiol state: not present), 41 monomers, 4525.233 × 2 Da Detail

MTRGTTDNLI PVYASILAAV VVGLVAYIAF KRWNSSKQNK Q

Total weight

9050.466 Da

Max. entity weight

4525.233 Da

Source organism

Rattus norvegicus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 80.3 %, Completeness (bb): 82.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.3 % (387 of 482)	89.1 % (220 of 247)	66.1 % (125 of 189)	91.3 % (42 of 46)
Backbone	82.0 % (200 of 244)	98.8 % (82 of 83)	64.5 % (78 of 121)	100.0 % (40 of 40)
Sidechain	80.9 % (224 of 277)	84.1 % (138 of 164)	78.5 % (84 of 107)	33.3 % (2 of 6)
Aromatic	15.8 % (6 of 38)	31.6 % (6 of 19)	0.0 % (0 of 18)	0.0 % (0 of 1)
Methyl	98.3 % (59 of 60)	100.0 % (30 of 30)	96.7 % (29 of 30)

1. entity

MTRGTTDNLI PVYASILAAV 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-C257A	[U-100% 13C; U-100% 15N]		1.5 mM
2	DPC	[U-98% 2H]		30 mM
3	sodium phosphate	natural abundance		20 mM

Protein Blocks Logo

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

Release date

2015-01-25

Citation

Structure of dimeric p75 neurotrophin receptor transmembrane domain provides insight on neurotrophin signaling
Nadezhdin, K., Arseniev, A., Goncharuk, S., Mineev, K., Vilar, M., Garc a-Carpio, I., Fernandez, E.
Not known

Related entities 1. p75-TM-C257A, : 1 : 2 : 17 entities Detail

Interaction partners 1. p75-TM-C257A, : 19 interactors Detail

More details for 19 interactors identified by 9 citations

Experiments performed 8 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-C257A	[U-100% 13C; U-100% 15N]		1.5 mM
2	DPC	[U-98% 2H]		30 mM
3	sodium phosphate	natural abundance		20 mM

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	p75-TM-C257A	[U-100% 13C; U-100% 15N]		1.5 mM
2	DPC	[U-98% 2H]		30 mM
3	sodium phosphate	natural abundance		20 mM

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	p75-TM-C257A	[U-100% 13C; U-100% 15N]		1.5 mM
2	DPC	[U-98% 2H]		30 mM
3	sodium phosphate	natural abundance		20 mM

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	p75-TM-C257A	[U-100% 13C; U-100% 15N]		1.5 mM
2	DPC	[U-98% 2H]		30 mM
3	sodium phosphate	natural abundance		20 mM

5 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-C257A	[U-100% 13C; U-100% 15N]		1.5 mM
2	DPC	[U-98% 2H]		30 mM
3	sodium phosphate	natural abundance		20 mM

6 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	p75-TM-C257A	[U-100% 13C; U-100% 15N]		1.5 mM
2	DPC	[U-98% 2H]		30 mM
3	sodium phosphate	natural abundance		20 mM

7 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-C257A	[U-100% 13C; U-100% 15N]		1.5 mM
2	DPC	[U-98% 2H]		30 mM
3	sodium phosphate	natural abundance		20 mM

8 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-C257A	[U-100% 13C; U-100% 15N]		1.5 mM
2	DPC	[U-98% 2H]		30 mM
3	sodium phosphate	natural abundance		20 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19741_2mjo.nef
Input source #2: Coordindates	2mjo.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-
MTRGTTDNLIPVYASILAAVVVGLVAYIAFKRWNSSKQNKQ
|||||||||||||||||||||||||||||||||||||||||
MTRGTTDNLIPVYASILAAVVVGLVAYIAFKRWNSSKQNKQ

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

-------110-------120-------130-------140-
MTRGTTDNLIPVYASILAAVVVGLVAYIAFKRWNSSKQNKQ
|||||||||||||||||||||||||||||||||||||||||
MTRGTTDNLIPVYASILAAVVVGLVAYIAFKRWNSSKQNKQ
--------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_19741_2mjo.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	387		100.0 (chain: A, length: 41)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	233 (1)	noe	90.2 (chain: A, length: 41)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	227 (227)	.	100.0 (chain: A, 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: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 220
  - ¹³C chemical shifts: 125
  - ¹⁵N chemical shifts: 42
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: 41, Sequence coverage: 90.2%
- Total number of restraints: 233
- Weight of restraints: 1.0 (233)
- Potential type of restraints: upper-bound-parabolic (233)
- Range of distance target values: 2.38, 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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 100.0%
- Total number of restraints: 227
- Total number of restraints per polymer type: 227
- Weight of restraints: 1.0 (227)
- Potential type of restraints: square-well-parabolic (227)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords dimer, membrane protein, p75, transmembrane