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BMRB: 18649

2LZ3

Transmembrane domain of Amyloid precursor protein WT

Authors

Chen, W., Wang, C.

Assembly

APPTM dimer

Entity

1. APPTM dimer (polymer, Thiol state: not present), 32 monomers, 3196.113 × 2 Da Detail

GAMAKGAIIG LMVGGVVIAT VIVITLVMLK KK

Total weight

6392.226 Da

Max. entity weight

3196.113 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.9 %, Completeness: 97.5 %, Completeness (bb): 95.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.5 % (352 of 361)	97.8 % (178 of 182)	98.0 % (144 of 147)	93.8 % (30 of 32)
Backbone	95.3 % (183 of 192)	94.2 % (65 of 69)	96.7 % (88 of 91)	93.8 % (30 of 32)
Sidechain	100.0 % (196 of 196)	100.0 % (113 of 113)	100.0 % (83 of 83)
Methyl	100.0 % (68 of 68)	100.0 % (34 of 34)	100.0 % (34 of 34)

1. wild type monomer

GAMAKGAIIG LMVGGVVIAT VIVITLVMLK KK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, 5% DPC, Pressure 1 atm, Temperature 313 K, pH 7.2, Details 5% DPC

#	Name	Isotope labeling	Type	Concentration
1	APPTM dimer	[U-100% 13C; U-100% 15N]		0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		0.5 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 21 models in PDB: 2LZ3, Strand ID: A, B Detail

Release date

2012-09-06

Citation

Familial Alzheimer's mutations within APPTM increase Aβ42 production by enhancing accessibility of ε-cleavage site
Chen, W., Gamache, E., Rosenman, D.J., Xie, J., Lopez, M.M., Li, Y., Wang, C.
Nat. Commun. (2014), 5, 3037-3037, PubMed 24390130 , DOI 10.1038/ncomms4037 , Abstract

Related entities 1. APPTM dimer, : 1 : 23 : 36 entities Detail

Interaction partners 1. APPTM dimer, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, 5% DPC, Pressure 1 atm, Temperature 313 K, pH 7.2, Details 5% DPC

#	Name	Isotope labeling	Type	Concentration
1	APPTM dimer	[U-100% 13C; U-100% 15N]		0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		0.5 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, 5% DPC, Pressure 1 atm, Temperature 313 K, pH 7.2, Details 5% DPC

#	Name	Isotope labeling	Type	Concentration
1	APPTM dimer	[U-100% 13C; U-100% 15N]		0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		0.5 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, 5% DPC, Pressure 1 atm, Temperature 313 K, pH 7.2, Details 5% DPC

#	Name	Isotope labeling	Type	Concentration
1	APPTM dimer	[U-100% 13C; U-100% 15N]		0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		0.5 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

4 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, 5% DPC, Pressure 1 atm, Temperature 313 K, pH 7.2, Details 5% DPC

#	Name	Isotope labeling	Type	Concentration
1	APPTM dimer	[U-100% 13C; U-100% 15N]		0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		0.5 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

5 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, 5% DPC, Pressure 1 atm, Temperature 313 K, pH 7.2, Details 5% DPC

#	Name	Isotope labeling	Type	Concentration
1	APPTM dimer	[U-100% 13C; U-100% 15N]		0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		0.5 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, 5% DPC, Pressure 1 atm, Temperature 313 K, pH 7.2, Details 5% DPC

#	Name	Isotope labeling	Type	Concentration
1	APPTM dimer	[U-100% 13C; U-100% 15N]		0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		0.5 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

7 3D HNHA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, 5% DPC, Pressure 1 atm, Temperature 313 K, pH 7.2, Details 5% DPC

#	Name	Isotope labeling	Type	Concentration
1	APPTM dimer	[U-100% 13C; U-100% 15N]		0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		0.5 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

8 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, 5% DPC, Pressure 1 atm, Temperature 313 K, pH 7.2, Details 5% DPC

#	Name	Isotope labeling	Type	Concentration
1	APPTM dimer	[U-100% 13C; U-100% 15N]		0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		0.5 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_18649_2lz3.nef
Input source #2: Coordindates	2lz3.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--
AMAKGAIIGLMVGGVVIATVIVITLVMLKKK
|||||||||||||||||||||||||||||||
AMAKGAIIGLMVGGVVIATVIVITLVMLKKK
--------10--------20--------30-

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

-------10--------20--------30--
AMAKGAIIGLMVGGVVIATVIVITLVMLKKK
|||||||||||||||||||||||||||||||
AMAKGAIIGLMVGGVVIATVIVITLVMLKKK
--------10--------20--------30-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	31	0	0	100.0
B	B	31	0	0	100.0

Content subtype: combined_18649_2lz3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	352		100.0 (chain: A, length: 31)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	710 (1)	noe	87.1 (chain: A, length: 31), 87.1 (chain: B, length: 31)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	90 (90)	.	87.1 (chain: A, length: 31), 87.1 (chain: B, length: 31)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	88 (88)	.	77.4 (chain: A, length: 31), 77.4 (chain: B, length: 31)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 178
  - ¹³C chemical shifts: 144
  - ¹⁵N chemical shifts: 30
- 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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 87.1%
  - Entity_assembly_ID: B, Chain length: 31, Sequence coverage: 87.1%
- Total number of restraints: 710
- Weight of restraints: 1.0 (710)
- Potential type of restraints: square-well-parabolic (710)
- Range of distance target values: 1.5, 3.0 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 87.1%
  - Entity_assembly_ID: B, Chain length: 31, Sequence coverage: 87.1%
- Total number of restraints: 90
- Total number of restraints per polymer type: 90
- Weight of restraints: 1.0 (90)
- Potential type of restraints: square-well-parabolic (90)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 77.4%
  - Entity_assembly_ID: B, Chain length: 31, Sequence coverage: 77.4%
- Total number of restraints: 88
- Potential type of restraints: undefined (88)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: B
    None