BMRBj - BMREntryMaster

Found 1 Document (3.607 seconds)

BMRB: 34455

8OTF

Mixing Abeta(1-40) and Abeta(1-42) peptides generates unique amyloid fibrils

Authors

Cerofolini, L., Ravera, E., Bologna, S., Wiglenda, T., Boddrich, A., Purfurst, B., Benilova, A., Korsak, M., Gallo, G., Rizzo, D., Gonnelli, L., Fragai, M., De Strooper, B., Wanker, E.E., Luchinat, C.

Assembly

Amyloid beta A4 protein

Entity

1. Amyloid beta A4 protein, entity 1 (polymer, Thiol state: not present), 40 monomers, 4329.801 × 8 Da Detail

DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV

2. Amyloid beta A4 protein, entity 2 (polymer, Thiol state: not present), 42 monomers, 4514.037 × 8 Da Detail

DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV IA

Total weight

70750.7 Da

Max. entity weight

4514.037 Da

Source organism

Homo sapiens

Exptl. method

solid-state NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.8 %, Completeness (bb): 99.7 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	93.8 % (423 of 451)	93.9 % (341 of 363)	93.2 % (82 of 88)
Backbone	99.7 % (315 of 316)	99.6 % (233 of 234)	100.0 % (82 of 82)
Sidechain	86.8 % (178 of 205)	89.4 % (178 of 199)	0.0 % (0 of 6)
Aromatic	60.0 % (30 of 50)	60.0 % (30 of 50)
Methyl	100.0 % (49 of 49)	100.0 % (49 of 49)

1. entity 1

DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV

2. entity 2

DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV IA

Show sample condition

Sample #1

Solvent system H2O, Pressure 1 atm, Temperature 283 K, pH 8.5, Details 50 uM [U-100% 13C; U-100% 15N] Amyloid-beta peptide 1-40, 50 uM Amyloid-beta peptide 1-42, 50 mM ammonium acetate, H2O

#	Name	Isotope labeling	Concentration
1	Amyloid-beta peptide 1-40	[U-100% 13C; U-100% 15N]	50 uM
2	Amyloid-beta peptide 1-42	natural abundance	50 uM
3	ammonium acetate	natural abundance	50 mM

Sample #2

Solvent system H2O, Pressure 1 atm, Temperature 283 K, pH 8.5, Details 70 uM [U-100% 13C; U-100% 15N] Amyloid-beta peptide 1-40, 30 uM Amyloid-beta peptide 1-42, 50 mM ammonium acetate, H2O

#	Name	Isotope labeling	Concentration
4	Amyloid-beta peptide 1-40	[U-100% 13C; U-100% 15N]	70 uM
5	Amyloid-beta peptide 1-42	natural abundance	30 uM
6	ammonium acetate	natural abundance	50 mM

Sample #3

Solvent system H2O, Pressure 1 atm, Temperature 283 K, pH 8.5, Details 50 uM Amyloid-beta peptide 1-40, 50 uM [U-100% 13C; U-100% 15N] Amyloid-beta peptide 1-42, 50 mM ammonium acetate, H2O

#	Name	Isotope labeling	Concentration
7	Amyloid-beta peptide 1-40	natural abundance	50 uM
8	Amyloid-beta peptide 1-42	[U-100% 13C; U-100% 15N]	50 uM
9	ammonium acetate	natural abundance	50 mM

Sample #4

Solvent system H2O, Pressure 1 atm, Temperature 283 K, pH 8.5, Details 50 uM [U-100% 13C] Amyloid-beta peptide 1-40, 50 uM [U-100% 15N] Amyloid-beta peptide 1-42, 50 mM ammonium acetate, H2O

#	Name	Isotope labeling	Concentration
10	Amyloid-beta peptide 1-40	[U-100% 13C]	50 uM
11	Amyloid-beta peptide 1-42	[U-100% 15N]	50 uM
12	ammonium acetate	natural abundance	50 mM

Protein Blocks Logo

Calculated from 4 models in PDB: 6TI6, Strand ID: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P Detail

Release date

2020-07-12

Citation

Mixing Aβ(1-40) and Aβ(1-42) peptides generates unique amyloid fibrils
Cerofolini, L., Ravera, E., Bologna, S., Wiglenda, T., Boddrich, A., Purfurst, B., Benilova, A., Korsak, M., Gallo, G., Rizzo, D., Gonnelli, L., Fragai, M., De Strooper, B., Wanker, E.E., Luchinat, C.
Chem. Commun. (Camb). (2020), 56, 8830-8833, PubMed 32749391 , DOI 10.1039/d0cc02463e , Abstract

Related entities 1. Amyloid beta A4 protein, entity 1, : 1 : 90 : 5 : 7 : 12 entities Detail

Related entities 2. Amyloid beta A4 protein, entity 2, : 1 : 44 : 3 : 54 : 13 entities Detail

Interaction partners 1. Amyloid beta A4 protein, entity 1, : 94 : 1 interactors Detail

More details for 95 interactors identified by 54 citations

Interaction partners 2. Amyloid beta A4 protein, entity 2, : 95 : 1 interactors Detail

More details for 96 interactors identified by 55 citations

Experiments performed 16 experiments Detail

1 2D 15N-13C NCA

Instrument

Bruker AVANCE III - 850 MHz

Sample

State anisotropic, Solvent system H2O, Pressure 1 atm, Temperature 283 K, pH 8.5, Details 50 uM [U-100% 13C; U-100% 15N] Amyloid-beta peptide 1-40, 50 uM Amyloid-beta peptide 1-42, 50 mM ammonium acetate, H2O

#	Name	Isotope labeling	Concentration
1	Amyloid-beta peptide 1-40	[U-100% 13C; U-100% 15N]	50 uM
2	Amyloid-beta peptide 1-42	natural abundance	50 uM
3	ammonium acetate	natural abundance	50 mM

2 2D 15N-13C NCO

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Amyloid-beta peptide 1-40	[U-100% 13C; U-100% 15N]	50 uM
2	Amyloid-beta peptide 1-42	natural abundance	50 uM
3	ammonium acetate	natural abundance	50 mM

3 3D NCACX

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Amyloid-beta peptide 1-40	[U-100% 13C; U-100% 15N]	50 uM
2	Amyloid-beta peptide 1-42	natural abundance	50 uM
3	ammonium acetate	natural abundance	50 mM

4 3D NCOCX

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Amyloid-beta peptide 1-40	[U-100% 13C; U-100% 15N]	50 uM
2	Amyloid-beta peptide 1-42	natural abundance	50 uM
3	ammonium acetate	natural abundance	50 mM

5 3D NCACB

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Amyloid-beta peptide 1-40	[U-100% 13C; U-100% 15N]	50 uM
2	Amyloid-beta peptide 1-42	natural abundance	50 uM
3	ammonium acetate	natural abundance	50 mM

6 3D N(CO)CACB

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Amyloid-beta peptide 1-40	[U-100% 13C; U-100% 15N]	50 uM
2	Amyloid-beta peptide 1-42	natural abundance	50 uM
3	ammonium acetate	natural abundance	50 mM

7 3D CANCO

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Amyloid-beta peptide 1-40	[U-100% 13C; U-100% 15N]	50 uM
2	Amyloid-beta peptide 1-42	natural abundance	50 uM
3	ammonium acetate	natural abundance	50 mM

8 2D 13C 13C SHANGHAI (15-300 ms)

Instrument

Bruker AVANCE II - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Amyloid-beta peptide 1-40	[U-100% 13C; U-100% 15N]	50 uM
2	Amyloid-beta peptide 1-42	natural abundance	50 uM
3	ammonium acetate	natural abundance	50 mM

9 2D 13C-13C PDSD (400, 800 ms)

Instrument

Bruker AVANCE II - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Amyloid-beta peptide 1-40	[U-100% 13C; U-100% 15N]	50 uM
2	Amyloid-beta peptide 1-42	natural abundance	50 uM
3	ammonium acetate	natural abundance	50 mM

10 2D 13C-15N PAIN (10 ms)

Instrument

Bruker AVANCE II - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Amyloid-beta peptide 1-40	[U-100% 13C; U-100% 15N]	50 uM
2	Amyloid-beta peptide 1-42	natural abundance	50 uM
3	ammonium acetate	natural abundance	50 mM

11 2D 15N-13C NCA

Instrument

Bruker AVANCE III - 850 MHz

Sample

State anisotropic, Solvent system H2O, Pressure 1 atm, Temperature 283 K, pH 8.5, Details 70 uM [U-100% 13C; U-100% 15N] Amyloid-beta peptide 1-40, 30 uM Amyloid-beta peptide 1-42, 50 mM ammonium acetate, H2O

#	Name	Isotope labeling	Concentration
4	Amyloid-beta peptide 1-40	[U-100% 13C; U-100% 15N]	70 uM
5	Amyloid-beta peptide 1-42	natural abundance	30 uM
6	ammonium acetate	natural abundance	50 mM

12 2D 13C-13C DARR (100 ms)

Instrument

Bruker AVANCE II - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
4	Amyloid-beta peptide 1-40	[U-100% 13C; U-100% 15N]	70 uM
5	Amyloid-beta peptide 1-42	natural abundance	30 uM
6	ammonium acetate	natural abundance	50 mM

13 2D 15N-13C NCA

Instrument

Bruker AVANCE III - 850 MHz

Sample

State anisotropic, Solvent system H2O, Pressure 1 atm, Temperature 283 K, pH 8.5, Details 50 uM Amyloid-beta peptide 1-40, 50 uM [U-100% 13C; U-100% 15N] Amyloid-beta peptide 1-42, 50 mM ammonium acetate, H2O

#	Name	Isotope labeling	Concentration
7	Amyloid-beta peptide 1-40	natural abundance	50 uM
8	Amyloid-beta peptide 1-42	[U-100% 13C; U-100% 15N]	50 uM
9	ammonium acetate	natural abundance	50 mM

14 2D 15N-13C NCO

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
7	Amyloid-beta peptide 1-40	natural abundance	50 uM
8	Amyloid-beta peptide 1-42	[U-100% 13C; U-100% 15N]	50 uM
9	ammonium acetate	natural abundance	50 mM

15 2D 13C-13C SHANGHAI (15-300 ms)

Instrument

Bruker AVANCE II - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
7	Amyloid-beta peptide 1-40	natural abundance	50 uM
8	Amyloid-beta peptide 1-42	[U-100% 13C; U-100% 15N]	50 uM
9	ammonium acetate	natural abundance	50 mM

16 2D 15N-13C hNhhC

Instrument

Bruker AVANCE III - 800 MHz

Sample

State anisotropic, Solvent system H2O, Pressure 1 atm, Temperature 283 K, pH 8.5, Details 50 uM [U-100% 13C] Amyloid-beta peptide 1-40, 50 uM [U-100% 15N] Amyloid-beta peptide 1-42, 50 mM ammonium acetate, H2O

#	Name	Isotope labeling	Concentration
10	Amyloid-beta peptide 1-40	[U-100% 13C]	50 uM
11	Amyloid-beta peptide 1-42	[U-100% 15N]	50 uM
12	ammonium acetate	natural abundance	50 mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34455_3.str
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

Content subtype: bmr34455_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	455		100.0 (chain: 2, length: 42), 100.0 (chain: 1, length: 40)
1	Chemical shift references	chem_shift_reference_1	OK	2		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 2, Chain length: 42, Sequence coverage: 100.0%

--------10--------20--------30--------40--
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA
||||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA

Entity_assembly_ID: 1, Chain length: 40, Sequence coverage: 100.0%

--------10--------20--------30--------40
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV

Total number of assignments
- ¹³C chemical shifts: 373
- ¹⁵N chemical shifts: 82

Completeness of assignments

Entity_assemble_ID: 2

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	ASP	CG	179.679
3	GLU	CD	180.565
4	PHE	CG	137.36
5	ARG	CZ	158.605
6	HIS	CG	132.086
7	ASP	CG	178.658
10	TYR	CG	127.481
11	GLU	CD	179.512
13	HIS	CG	137.554
14	HIS	CG	132.667
15	GLN	CD	179.181
19	PHE	CG	137.92
20	PHE	CG	137.701
22	GLU	CD	182.579
23	ASP	CG	179.792

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	186	176	94.6
¹⁵N chemical shifts	45	42	93.3

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	84	84	100.0
¹⁵N chemical shifts	42	42	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	102	92	90.2
¹⁵N chemical shifts	3	0	0.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	27	27	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	25	15	60.0

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	ASP	CG	179.54
3	GLU	CD	180.565
4	PHE	CG	137.523
5	ARG	CZ	158.633
6	HIS	CG	131.642
7	ASP	CG	178.973
10	TYR	CG	127.497
11	GLU	CD	179.473
13	HIS	CG	137.361
14	HIS	CG	132.854
15	GLN	CD	178.891
19	PHE	CG	137.889
20	PHE	CG	137.825
22	GLU	CD	182.622
23	ASP	CG	179.892

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	177	167	94.4
¹⁵N chemical shifts	43	40	93.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	80	80	100.0
¹⁵N chemical shifts	40	40	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	97	87	89.7
¹⁵N chemical shifts	3	0	0.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	24	24	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	25	15	60.0

Tautomeric state of HIS
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: 2
- Chain_ID: 1

Keywords amyloid beta peptides Alzheimer's disease solid-state NMR supramolecular assembly, protein fibril

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Found 1 Document (3.607 seconds)

BMRB: 34455

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. Amyloid beta A4 protein, entity 1, : 1 : 90 : 5 : 7 : 12 entities Detail

Related entities 2. Amyloid beta A4 protein, entity 2, : 1 : 44 : 3 : 54 : 13 entities Detail

Interaction partners 1. Amyloid beta A4 protein, entity 1, : 94 : 1 interactors Detail

Interaction partners 2. Amyloid beta A4 protein, entity 2, : 95 : 1 interactors Detail

Experiments performed 16 experiments Detail

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Chemical shift validation 4 contents Detail