BMRBj - BMREntryMaster

Found 1 Document (1.173 seconds)

BMRB: 25818

2N7R

Structure of the transmembrane domain of human nicastrin in DPC micelles

Authors

Li, Y., Liew, L., Li, Q., Kang, C.

Assembly

transmembrane domain of human nicastrin in DPC micelles

Entity

1. transmembrane domain of human nicastrin in DPC micelles (polymer, Thiol state: all free), 54 monomers, 5982.927 Da Detail

MAHHHHHHAS KELELITLTV GFGILIFSLI VTYCINAKAD VLFIAPREPG AVSY

Formula weight

5982.927 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 85.2 %, Completeness: 57.3 %, Completeness (bb): 78.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	57.3 % (359 of 627)	60.8 % (192 of 316)	47.3 % (122 of 258)	84.9 % (45 of 53)
Backbone	78.8 % (252 of 320)	80.7 % (88 of 109)	75.5 % (120 of 159)	84.6 % (44 of 52)
Sidechain	39.7 % (142 of 358)	50.2 % (104 of 207)	24.7 % (37 of 150)	100.0 % (1 of 1)
Aromatic	2.9 % (2 of 70)	5.7 % (2 of 35)	0.0 % (0 of 35)
Methyl	46.3 % (38 of 82)	75.6 % (31 of 41)	17.1 % (7 of 41)

1. transmembrane domain of human nicastrin

MAHHHHHHAS KELELITLTV GFGILIFSLI VTYCINAKAD VLFIAPREPG AVSY

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	transmembrane domain of human nicastrin	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	DPC	natural abundance		200 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.14 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.14 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.07 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.65 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N7R, Strand ID: A Detail

Release date

2016-04-24

Citation

Structure of the transmembrane domain of human nicastrin-a component of γ-secretase
Li, Y., Liew, L., Li, Q., Kang, C.
Sci. Rep. (2016), 6, 19522-19522, PubMed 26776682 , DOI 10.1038/srep19522 , Abstract

Related entities 1. transmembrane domain of human nicastrin in DPC micelles, : 1 : 1 : 7 : 5 entities Detail

Interaction partners 1. transmembrane domain of human nicastrin in DPC micelles, : 21 interactors Detail

More details for 21 interactors identified by 8 citations

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	transmembrane domain of human nicastrin	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	DPC	natural abundance		200 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	transmembrane domain of human nicastrin	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	DPC	natural abundance		200 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	transmembrane domain of human nicastrin	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	DPC	natural abundance		200 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

4 3D HN(CO)CACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	transmembrane domain of human nicastrin	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	DPC	natural abundance		200 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	transmembrane domain of human nicastrin	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	DPC	natural abundance		200 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	transmembrane domain of human nicastrin	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	DPC	natural abundance		200 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	transmembrane domain of human nicastrin	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	DPC	natural abundance		200 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25818_2n7r.nef
Input source #2: Coordindates	2n7r.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------
MAHHHHHHASKELELITLTVGFGILIFSLIVTYCINAKADVLFIAPREPGAVSY
||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAHHHHHHASKELELITLTVGFGILIFSLIVTYCINAKADVLFIAPREPGAVSY
--------10--------20--------30--------40--------50----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	54	0	0	100.0

Content subtype: combined_25818_2n7r.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	375		85.2 (chain: A, length: 54)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	318 (1)	noe	79.6 (chain: A, length: 54)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	100 (100)	.	83.3 (chain: A, length: 54)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 85.2%
- Total number of assignments
  - ¹H chemical shifts: 210
  - ¹³C chemical shifts: 120
  - ¹⁵N chemical shifts: 45
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 79.6%
- Total number of restraints: 318
- Weight of restraints: 1.0 (318)
- Potential type of restraints: square-well-parabolic (318)
- Range of distance target values: 2.27, 3.86 (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: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 83.3%
- Total number of restraints: 100
- Total number of restraints per polymer type: 100
- Weight of restraints: 1.0 (100)
- Potential type of restraints: square-well-parabolic (100)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Membrnae Protein, gamma-secretase, nicastrin, nmr