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Found 1 Document (3.193 seconds)

BMRB: 19009

2M4J

40-residue beta-amyloid fibril derived from Alzheimer's disease brain

Authors

Lu, J., Qiang, W., Meredith, S.C., Yau, W., Schweiters, C.D., Tycko, R.

Assembly

40-residue beta-amyloid fibril

Entity

1. 40-residue beta-amyloid fibril (polymer, Thiol state: not present), 40 monomers, 4329.801 × 9 Da Detail

DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV

Total weight

38968.207 Da

Max. entity weight

4329.801 Da

Source organism

Homo sapiens

Exptl. method

NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.5 %, Completeness: 91.8 %, Completeness (bb): 96.8 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	91.8 % (201 of 219)	90.4 % (160 of 177)	97.6 % (41 of 42)
Backbone	96.8 % (149 of 154)	96.5 % (110 of 114)	97.5 % (39 of 40)
Sidechain	85.9 % (85 of 99)	85.6 % (83 of 97)	100.0 % (2 of 2)
Aromatic	48.0 % (12 of 25)	48.0 % (12 of 25)
Methyl	100.0 % (23 of 23)	100.0 % (23 of 23)

1. beta-amyloid peptide

DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV

Show sample condition

Sample

Solvent system none, Pressure 1 atm, Temperature 273 K, pH 7.4, Details 40-residue beta-amyloid peptide seeded with amyloid extracted from brain tissue. Lyophilized, then rehydrated after packing in MAS rotor.

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid peptide	selectively and uniformly labeled samples		1.0 ~ 2.0 mg

Protein Blocks Logo

Calculated from 20 models in PDB: 2M4J, Strand ID: A, B, C, D, E, F, G, H, I Detail

Release date

2013-02-18

Citation

Molecular structure of β-amyloid fibrils in Alzheimer's disease brain tissue
Lu, J., Qiang, W., Yau, W., Schweiters, C.D., Meredith, S.C., Tycko, R.
Cell (2013), 154, 1257-1268, PubMed 24034249 , DOI 10.1016/j.cell.2013.08.035 , Abstract

Related entities 1. 40-residue beta-amyloid fibril, : 1 : 90 : 5 : 7 : 17 entities Detail

Interaction partners 1. 40-residue beta-amyloid fibril, : 95 interactors Detail

More details for 95 interactors identified by 54 citations

Experiments performed 13 experiments Detail

1 2D 13C-13C with fpRFDR

Instrument

Varian InfinityPlus - 600 MHz

Sample

State solid, Solvent system none, Pressure 1 atm, Temperature 273 K, pH 7.4, Details 40-residue beta-amyloid peptide seeded with amyloid extracted from brain tissue. Lyophilized, then rehydrated after packing in MAS rotor.

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid peptide	selectively and uniformly labeled samples		1.0 ~ 2.0 mg

2 2D and 3D NCACX

Instrument

Varian InfinityPlus - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid peptide	selectively and uniformly labeled samples		1.0 ~ 2.0 mg

3 2D NCOCX

Instrument

Varian InfinityPlus - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid peptide	selectively and uniformly labeled samples		1.0 ~ 2.0 mg

4 3D NCOCX

Instrument

Varian Infinity - 750 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid peptide	selectively and uniformly labeled samples		1.0 ~ 2.0 mg

5 2D NCACX

Instrument

Varian Infinity - 750 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid peptide	selectively and uniformly labeled samples		1.0 ~ 2.0 mg

6 2D 13C-13C with spin diffusion

Instrument

Varian Infinity - 750 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid peptide	selectively and uniformly labeled samples		1.0 ~ 2.0 mg

7 2D 13C-13C with RAD

Instrument

Varian InfinityPlus - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid peptide	selectively and uniformly labeled samples		1.0 ~ 2.0 mg

8 2D 13C-13C with PAR

Instrument

Varian InfinityPlus - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid peptide	selectively and uniformly labeled samples		1.0 ~ 2.0 mg

9 2D 15N-13C TEDOR

Instrument

Varian InfinityPlus - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid peptide	selectively and uniformly labeled samples		1.0 ~ 2.0 mg

10 2D 15N-13C TEDOR

Instrument

Varian Infinity - 750 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid peptide	selectively and uniformly labeled samples		1.0 ~ 2.0 mg

11 15N- and 13C-BARE

Instrument

Varian InfinityPlus - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid peptide	selectively and uniformly labeled samples		1.0 ~ 2.0 mg

12 13C PITHIRDS-CT

Instrument

Varian InfinityPlus - 400 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid peptide	selectively and uniformly labeled samples		1.0 ~ 2.0 mg

13 2D 13C-13C with fpRFDR

Instrument

Varian Infinity - 750 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid peptide	selectively and uniformly labeled samples		1.0 ~ 2.0 mg

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19009_2m4j.nef
Input source #2: Coordindates	2m4j.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
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	40	100.0
B	B	40	100.0
C	C	40	100.0
D	D	40	100.0
E	E	40	100.0
F	F	40	100.0
G	G	40	100.0
H	H	40	100.0
I	I	40	100.0

Content subtype: combined_19009_2m4j.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	216		97.5 (chain: A, length: 40)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	42 (1)	noe	30.0 (chain: B, length: 40), 30.0 (chain: C, length: 40), 30.0 (chain: D, length: 40)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	20 (1)	noe	30.0 (chain: A, length: 40)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	423 (1)	noe	95.0 (chain: A, length: 40)
4	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	6 (1)	noe	7.5 (chain: B, length: 40), 7.5 (chain: C, length: 40), 7.5 (chain: D, length: 40)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	60 (60)	.	100.0 (chain: B, length: 40)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 97.5%

--------10--------20--------30--------40
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
||||||||||||| ||||||||||||||||||||||||||
DAEFRHDSGYEVH.QKLVFFAEDVGSNKGAIIGLMVGGVV

Total number of assignments
- ¹³C chemical shifts: 175
- ¹⁵N chemical shifts: 41

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	ASP	CG	178.2
3	GLU	CD	182.0
5	ARG	CZ	159.2
6	HIS	CG	136.8
7	ASP	CG	180.0
10	TYR	CG	129.1
10	TYR	CZ	157.7
11	GLU	CD	183.3
13	HIS	CG	139.4
15	GLN	CD	176.3
19	PHE	CG	142.2
20	PHE	CG	141.7
22	GLU	CD	181.9
23	ASP	CG	178.0
27	ASN	CG	182.1

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	177	160	90.4
¹⁵N chemical shifts	43	41	95.3

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	80	77	96.3
¹⁵N chemical shifts	40	39	97.5

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	97	83	85.6
¹⁵N chemical shifts	3	2	66.7

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	12	48.0

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: A

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 30.0%
  - Entity_assembly_ID: C, Chain length: 40, Sequence coverage: 30.0%
  - Entity_assembly_ID: D, Chain length: 40, Sequence coverage: 30.0%
- Total number of restraints: 42
- Weight of restraints: 1.0 (42)
- Potential type of restraints: square-well-parabolic (42)
- Range of distance target values: 2.95, 5.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D
  - Chain_ID: E
    None
  - Chain_ID: F
    None
  - Chain_ID: G
    None
  - Chain_ID: H
    None
  - Chain_ID: I
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 30.0%
  - Total number of restraints: 20
  - Weight of restraints: 1.0 (20)
  - Potential type of restraints: square-well-parabolic (20)
  - Range of distance target values: 4.5, 4.5 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
    - Chain_ID: C
      None
    - Chain_ID: D
      None
    - Chain_ID: E
      None
    - Chain_ID: F
      None
    - Chain_ID: G
      None
    - Chain_ID: H
      None
    - Chain_ID: I
      None
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_5
    - Status: OK
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 95.0%
    - Total number of restraints: 423
    - Weight of restraints: 1.0 (423)
    - Potential type of restraints: square-well-parabolic (423)
    - Range of distance target values: 3.5, 5.5 (Å)
    - Histogram of distance target values
    - Histogram of discrepancy in distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
      - Chain_ID: C
        None
      - Chain_ID: D
        None
      - Chain_ID: E
        None
      - Chain_ID: F
        None
      - Chain_ID: G
        None
      - Chain_ID: H
        None
      - Chain_ID: I
        None
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_4
      - Status: Warning
      - Experiment type: noe
      - Sequence coverage of experimental data
        Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 7.5%
        Entity_assembly_ID: C, Chain length: 40, Sequence coverage: 7.5%
        Entity_assembly_ID: D, Chain length: 40, Sequence coverage: 7.5%
      - Total number of restraints: 6
        Inter-chain restraints: 1
        Symmetric restraints: 5
      - Weight of restraints: 1.0 (6)
        Inter-chain restraints: 1.0 (1)
        Symmetric restraints: 1.0 (5)
      - Potential type of restraints: square-well-parabolic (6)
        Inter-chain restraints: square-well-parabolic (1)
        Symmetric restraints: square-well-parabolic (5)
      - Range of distance target values: 8.0, 30.0 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
        None
        Chain_ID: B
        Chain_ID: C
        Chain_ID: D
        Chain_ID: E
        None
        Chain_ID: F
        None
        Chain_ID: G
        None
        Chain_ID: H
        None
        Chain_ID: I
        None
      - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 100.0%
- Total number of restraints: 60
- Total number of restraints per polymer type: 60
- Weight of restraints: 1.0 (60)
- Potential type of restraints: square-well-parabolic (60)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: B

Keywords Alzheimer's disease, amyloid, solid state NMR

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Found 1 Document (3.193 seconds)

BMRB: 19009

Sample

Related entities 1. 40-residue beta-amyloid fibril, : 1 : 90 : 5 : 7 : 17 entities Detail

Interaction partners 1. 40-residue beta-amyloid fibril, : 95 interactors Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 7 contents Detail