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BMRB: 18080

2LLM

structure of amyloid precursor protein's transmembrane domain

Authors

Nadezhdin, K.D., Bocharova, O.V., Bocharov, E.V., Arseniev, A.A.

Assembly

amyloid precursor protein's transmembrane domain

Entity

1. amyloid precursor protein's transmembrane domain (polymer, Thiol state: not present), 43 monomers, 4445.418 Da Detail

GSQKLVFFAE DVGSNKGAII GLMVGGVVIA TVIVITLVML KKK

Formula weight

4445.418 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 77.8 %, Completeness (bb): 83.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.8 % (386 of 496)	79.4 % (200 of 252)	71.4 % (142 of 199)	97.8 % (44 of 45)
Backbone	83.3 % (215 of 258)	98.9 % (91 of 92)	66.7 % (82 of 123)	97.7 % (42 of 43)
Sidechain	74.9 % (206 of 275)	68.1 % (109 of 160)	84.1 % (95 of 113)	100.0 % (2 of 2)
Aromatic	20.0 % (4 of 20)	40.0 % (4 of 10)	0.0 % (0 of 10)
Methyl	93.6 % (73 of 78)	94.9 % (37 of 39)	92.3 % (36 of 39)

1. entity

GSQKLVFFAE DVGSNKGAII GLMVGGVVIA TVIVITLVML KKK

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 4.6, Details APPjmtm = peptide under investigations

#	Name	Isotope labeling	Type	Concentration
1	APPjmtm	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	DPC	[U-100% 2H]		21.0 ~ 70.0 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 4.6

#	Name	Isotope labeling	Type	Concentration
5	APPjmtm	[U-100% 15N]		0.3 ~ 1.0 mM
6	DPC	natural abundance		21.0 ~ 70.0 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %

Protein Blocks Logo

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

Release date

2012-01-24

Citation

Structural and dynamic study of the transmembrane domain of the amyloid precursor protein
Nadezhdin, K.D., Bocharova, O.V., Bocharov, E.V., Arseniev, A.A.
Acta Naturae (2011), 3, 69-76, PubMed 22649674 , DOI: , Abstract

Related entities 1. amyloid precursor protein's transmembrane domain, : 1 : 1 : 20 : 14 entities Detail

Interaction partners 1. amyloid precursor protein's transmembrane domain, : 96 interactors Detail

More details for 96 interactors identified by 54 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 4.6, Details APPjmtm = peptide under investigations

#	Name	Isotope labeling	Type	Concentration
1	APPjmtm	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	DPC	[U-100% 2H]		21.0 ~ 70.0 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 4.6, Details APPjmtm = peptide under investigations

#	Name	Isotope labeling	Type	Concentration
1	APPjmtm	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	DPC	[U-100% 2H]		21.0 ~ 70.0 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

3 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 4.6, Details APPjmtm = peptide under investigations

#	Name	Isotope labeling	Type	Concentration
1	APPjmtm	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	DPC	[U-100% 2H]		21.0 ~ 70.0 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

4 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 4.6, Details APPjmtm = peptide under investigations

#	Name	Isotope labeling	Type	Concentration
1	APPjmtm	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	DPC	[U-100% 2H]		21.0 ~ 70.0 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

5 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 4.6, Details APPjmtm = peptide under investigations

#	Name	Isotope labeling	Type	Concentration
1	APPjmtm	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	DPC	[U-100% 2H]		21.0 ~ 70.0 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 4.6, Details APPjmtm = peptide under investigations

#	Name	Isotope labeling	Type	Concentration
1	APPjmtm	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	DPC	[U-100% 2H]		21.0 ~ 70.0 mM
3	H2O	natural abundance		95 %
4	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 273 K, pH 4.6, Details APPjmtm = peptide under investigations

#	Name	Isotope labeling	Type	Concentration
1	APPjmtm	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	DPC	[U-100% 2H]		21.0 ~ 70.0 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

8 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 4.6

#	Name	Isotope labeling	Type	Concentration
5	APPjmtm	[U-100% 15N]		0.3 ~ 1.0 mM
6	DPC	natural abundance		21.0 ~ 70.0 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 4.6

#	Name	Isotope labeling	Type	Concentration
5	APPjmtm	[U-100% 15N]		0.3 ~ 1.0 mM
6	DPC	natural abundance		21.0 ~ 70.0 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %

10 3D 1H-15N TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 4.6

#	Name	Isotope labeling	Type	Concentration
5	APPjmtm	[U-100% 15N]		0.3 ~ 1.0 mM
6	DPC	natural abundance		21.0 ~ 70.0 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18080_2llm.nef
Input source #2: Coordindates	2llm.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---
GSQKLVFFAEDVGSNKGAIIGLMVGGVVIATVIVITLVMLKKK
|||||||||||||||||||||||||||||||||||||||||||
GSQKLVFFAEDVGSNKGAIIGLMVGGVVIATVIVITLVMLKKK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	43	0	0	100.0

Content subtype: combined_18080_2llm.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	381		100.0 (chain: A, length: 43)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	323 (1)	noe	95.3 (chain: A, length: 43)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 43, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 199
  - ¹³C chemical shifts: 138
  - ¹⁵N chemical shifts: 44
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 43, Sequence coverage: 95.3%
- Total number of restraints: 323
- Weight of restraints: 1.0 (323)
- Potential type of restraints: upper-bound-parabolic (323)
- Range of distance target values: 2.72, 5.5 (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

Keywords Alzheimer's disease, amyloid precursor protein, DPC micelles, solution NMR