BMRBj - BMREntryMaster

Found 1 Document (2.189 seconds)

BMRB: 34396

7O1Q

Structure of pore-forming amyloid-beta tetramers

Authors

Bardiaux, B., Ciudad, S., Carulla, N.

Assembly

Amyloid beta A4 protein

Entity

1. Amyloid beta A4 protein (polymer, Thiol state: not present), 42 monomers, 4514.037 × 4 Da Detail

DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV IA

Total weight

18056.148 Da

Max. entity weight

4514.037 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealingsimulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.6 %, Completeness: 42.7 %, Completeness (bb): 78.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	42.7 % (199 of 466)	21.2 % (50 of 236)	59.7 % (111 of 186)	86.4 % (38 of 44)
Backbone	78.2 % (197 of 252)	53.3 % (48 of 90)	92.5 % (111 of 120)	90.5 % (38 of 42)
Sidechain	14.4 % (36 of 250)	1.4 % (2 of 146)	33.3 % (34 of 102)	0.0 % (0 of 2)
Aromatic	0.0 % (0 of 50)	0.0 % (0 of 25)	0.0 % (0 of 25)
Methyl	7.7 % (4 of 52)	0.0 % (0 of 26)	15.4 % (4 of 26)

1. entity 1

DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV IA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 8.5, Details 1 mM [U-15N] Amyloid-beta A4 protein, 10 mM [U-2H] TRIS-d11, 28.5 mM [U-2H] DPC-d38, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Amyloid-beta A4 protein	[U-15N]	1 mM
2	TRIS-d11	[U-2H]	10 mM
3	DPC-d38	[U-2H]	28.5 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 8.5, Details 1 mM [U-13C; U-15N; U-2H] Amyloid-beta A4 protein, 10 mM [U-2H] TRIS-d11, 28.5 mM [U-2H] DPC-d38, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Amyloid-beta A4 protein	[U-13C; U-15N; U-2H]	1 mM
5	TRIS-d11	[U-2H]	10 mM
6	DPC-d38	[U-2H]	28.5 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 8.5, Details 1 mM [U-2H,13C,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR Amyloid-beta A4 protein, 10 mM [U-2H] TRIS-d11, 28.5 mM [U-2H] DPC-d38, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	Amyloid-beta A4 protein	[U-2H,13C,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR	1 mM
8	TRIS-d11	[U-2H]	10 mM
9	DPC-d38	[U-2H]	28.5 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 8.5, Details 1 mM [U-2H,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR Amyloid-beta A4 protein, 10 mM [U-2H] TRIS-d11, 28.5 mM [U-2H] DPC-d38, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
10	Amyloid-beta A4 protein	[U-2H,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR	1 mM
11	TRIS-d11	[U-2H]	10 mM
12	DPC-d38	[U-2H]	28.5 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 2.93 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 2.93 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 4.32 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 6RHY, Strand ID: A, B, C, D Detail

Release date

2019-09-24

Citation

Aβ(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage
Ciudad, S., Puig, E., Botzanowski, T., Meigooni, M., Arango, A.S., Do, J., Mayzel, M., Bayoumi, M., Chaignepain, S., Maglia, G., Cianferani, S., Orekhov, V., Tajkhorshid, E., Bardiaux, B., Carulla, N.
Nat. Commun. (2020), 11, 3014-3014, PubMed 32541820 , DOI 10.1038/s41467-020-16566-1 , Abstract

Related entities 1. Amyloid beta A4 protein, : 1 : 44 : 3 : 54 : 14 entities Detail

Interaction partners 1. Amyloid beta A4 protein, : 96 interactors Detail

More details for 96 interactors identified by 55 citations

Experiments performed 23 experiments Detail

1 2D 1H-15N TROSY

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 9.5, Details 1 mM [U-15N] Amyloid-beta A4 protein, 10 mM [U-2H] TRIS-d11, 28.5 mM [U-2H] DPC-d38, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Amyloid-beta A4 protein	[U-15N]	1 mM
2	TRIS-d11	[U-2H]	10 mM
3	DPC-d38	[U-2H]	28.5 mM

2 3D HNCA

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 9.5, Details 1 mM [U-13C; U-15N; U-2H] Amyloid-beta A4 protein, 10 mM [U-2H] TRIS-d11, 28.5 mM [U-2H] DPC-d38, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Amyloid-beta A4 protein	[U-13C; U-15N; U-2H]	1 mM
5	TRIS-d11	[U-2H]	10 mM
6	DPC-d38	[U-2H]	28.5 mM

3 3D HNCO

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 8.5, Details 1 mM [U-13C; U-15N; U-2H] Amyloid-beta A4 protein, 10 mM [U-2H] TRIS-d11, 28.5 mM [U-2H] DPC-d38, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Amyloid-beta A4 protein	[U-13C; U-15N; U-2H]	1 mM
5	TRIS-d11	[U-2H]	10 mM
6	DPC-d38	[U-2H]	28.5 mM

4 3D HN(CO)CA

Instrument

Bruker AVANCE III - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
4	Amyloid-beta A4 protein	[U-13C; U-15N; U-2H]	1 mM
5	TRIS-d11	[U-2H]	10 mM
6	DPC-d38	[U-2H]	28.5 mM

5 3D HNCACB

Instrument

Bruker AVANCE III - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
4	Amyloid-beta A4 protein	[U-13C; U-15N; U-2H]	1 mM
5	TRIS-d11	[U-2H]	10 mM
6	DPC-d38	[U-2H]	28.5 mM

6 3D HN(COCA)CB

Instrument

Bruker AVANCE III - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
4	Amyloid-beta A4 protein	[U-13C; U-15N; U-2H]	1 mM
5	TRIS-d11	[U-2H]	10 mM
6	DPC-d38	[U-2H]	28.5 mM

7 3D 13C-HMQC-[1H,1H]-NOESY-13C-HMQC

Instrument

Bruker AVANCE III - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
4	Amyloid-beta A4 protein	[U-13C; U-15N; U-2H]	1 mM
5	TRIS-d11	[U-2H]	10 mM
6	DPC-d38	[U-2H]	28.5 mM

8 3D (Hme)Cme([C]CA)CO

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 8.5, Details 1 mM [U-2H,13C,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR Amyloid-beta A4 protein, 10 mM [U-2H] TRIS-d11, 28.5 mM [U-2H] DPC-d38, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	Amyloid-beta A4 protein	[U-2H,13C,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR	1 mM
8	TRIS-d11	[U-2H]	10 mM
9	DPC-d38	[U-2H]	28.5 mM

9 3D (Hme)Cme([C]CA)NH

Instrument

Bruker AVANCE III - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
7	Amyloid-beta A4 protein	[U-2H,13C,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR	1 mM
8	TRIS-d11	[U-2H]	10 mM
9	DPC-d38	[U-2H]	28.5 mM

10 3D Hme(Cme[C]CA)NH

Instrument

Bruker AVANCE III - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
7	Amyloid-beta A4 protein	[U-2H,13C,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR	1 mM
8	TRIS-d11	[U-2H]	10 mM
9	DPC-d38	[U-2H]	28.5 mM

11 3D (H)C-TOCSY-C-TOCSY-(C)H

Instrument

Bruker AVANCE III - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
7	Amyloid-beta A4 protein	[U-2H,13C,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR	1 mM
8	TRIS-d11	[U-2H]	10 mM
9	DPC-d38	[U-2H]	28.5 mM

12 3D Hm-CmHm NOESY

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 8.5, Details 1 mM [U-2H,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR Amyloid-beta A4 protein, 10 mM [U-2H] TRIS-d11, 28.5 mM [U-2H] DPC-d38, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
10	Amyloid-beta A4 protein	[U-2H,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR	1 mM
11	TRIS-d11	[U-2H]	10 mM
12	DPC-d38	[U-2H]	28.5 mM

13 3D Cm-CmHm NOESY

Instrument

Bruker AVANCE III - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
10	Amyloid-beta A4 protein	[U-2H,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR	1 mM
11	TRIS-d11	[U-2H]	10 mM
12	DPC-d38	[U-2H]	28.5 mM

14 3D Hm-NH NOESY

Instrument

Bruker AVANCE III - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
10	Amyloid-beta A4 protein	[U-2H,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR	1 mM
11	TRIS-d11	[U-2H]	10 mM
12	DPC-d38	[U-2H]	28.5 mM

15 3D Cm-NH NOESY

Instrument

Bruker AVANCE III - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
10	Amyloid-beta A4 protein	[U-2H,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR	1 mM
11	TRIS-d11	[U-2H]	10 mM
12	DPC-d38	[U-2H]	28.5 mM

16 2D 1H-15N TROSY

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 8.5, Details 1 mM [U-15N] Amyloid-beta A4 protein, 10 mM [U-2H] TRIS-d11, 28.5 mM [U-2H] DPC-d38, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Amyloid-beta A4 protein	[U-15N]	1 mM
2	TRIS-d11	[U-2H]	10 mM
3	DPC-d38	[U-2H]	28.5 mM

17 3D HNCA

Instrument

Bruker AVANCE - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
4	Amyloid-beta A4 protein	[U-13C; U-15N; U-2H]	1 mM
5	TRIS-d11	[U-2H]	10 mM
6	DPC-d38	[U-2H]	28.5 mM

18 3D HNCACB

Instrument

Bruker AVANCE - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
4	Amyloid-beta A4 protein	[U-13C; U-15N; U-2H]	1 mM
5	TRIS-d11	[U-2H]	10 mM
6	DPC-d38	[U-2H]	28.5 mM

19 3D 13C-HMQC-[1H,1H]-NOESY-13C-HMQC

Instrument

Bruker AVANCE III - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
4	Amyloid-beta A4 protein	[U-13C; U-15N; U-2H]	1 mM
5	TRIS-d11	[U-2H]	10 mM
6	DPC-d38	[U-2H]	28.5 mM

20 3D Hm-CmHm NOESY

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 9.5, Details 1 mM [U-2H,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR Amyloid-beta A4 protein, 10 mM [U-2H] TRIS-d11, 28.5 mM [U-2H] DPC-d38, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
10	Amyloid-beta A4 protein	[U-2H,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR	1 mM
11	TRIS-d11	[U-2H]	10 mM
12	DPC-d38	[U-2H]	28.5 mM

21 3D Cm-CmHm NOESY

Instrument

Bruker AVANCE III - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
10	Amyloid-beta A4 protein	[U-2H,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR	1 mM
11	TRIS-d11	[U-2H]	10 mM
12	DPC-d38	[U-2H]	28.5 mM

22 3D Hm-NH NOESY

Instrument

Bruker AVANCE III - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
10	Amyloid-beta A4 protein	[U-2H,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR	1 mM
11	TRIS-d11	[U-2H]	10 mM
12	DPC-d38	[U-2H]	28.5 mM

23 3D Cm-NH NOESY

Instrument

Bruker AVANCE III - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
10	Amyloid-beta A4 protein	[U-2H,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR	1 mM
11	TRIS-d11	[U-2H]	10 mM
12	DPC-d38	[U-2H]	28.5 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34396_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: bmr34396_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	632		95.2 (chain: 1, length: 42)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 42, Sequence coverage: 95.2%
- Total number of assignments
  - ¹³C chemical shifts: 368
  - ¹H chemical shifts: 132
  - ¹⁵N chemical shifts: 132
- Completeness of assignments
  - Entity_assemble_ID: 1
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	186	108	58.1
¹H chemical shifts	236	37	15.7
¹⁵N chemical shifts	45	37	82.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	84	75	89.3
¹H chemical shifts	90	37	41.1
¹⁵N chemical shifts	42	37	88.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	102	33	32.4
¹H chemical shifts	146	0	0.0
¹⁵N chemical shifts	3	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	27	4	14.8
¹H chemical shifts	27	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	25	0	0.0
¹H chemical shifts	25	0	0.0

Keywords AMYLOID, Alzheimer's disease, PROTEIN FIBRIL, membrane pore, oligomer

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Found 1 Document (2.189 seconds)

BMRB: 34396

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Amyloid beta A4 protein, : 1 : 44 : 3 : 54 : 14 entities Detail

Interaction partners 1. Amyloid beta A4 protein, : 96 interactors Detail

Experiments performed 23 experiments Detail

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