BMRBj - BMREntryMaster

Found 1 Document (3.219 seconds)

BMRB: 18127

2LMN

Structural Model for a 40-Residue Beta-Amyloid Fibril with Two-Fold Symmetry, Positive Stagger

Authors

Tycko, R., Petkova, A.

Assembly

40-Residue Beta-Amyloid Fibril with Two-Fold Symmetry

Entity

1. 40-Residue Beta-Amyloid Fibril with Two-Fold Symmetry (polymer, Thiol state: not present), 40 monomers, 4329.801 × 12 Da Detail

DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV

Total weight

51957.61 Da

Max. entity weight

4329.801 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 85.0 %, Completeness: 51.6 %, Completeness (bb): 73.4 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	51.6 % (113 of 219)	53.7 % (95 of 177)	42.9 % (18 of 42)
Backbone	73.4 % (113 of 154)	83.3 % (95 of 114)	45.0 % (18 of 40)
Sidechain	28.3 % (28 of 99)	28.9 % (28 of 97)	0.0 % (0 of 2)
Aromatic	0.0 % (0 of 25)	0.0 % (0 of 25)
Methyl	13.0 % (3 of 23)	13.0 % (3 of 23)

1. beta-amyloid

DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV

Show sample condition

Sample

Solvent system 10 mM phosphate buffer, Pressure 1 atm, Temperature 300 K, pH 7.4, Details grown at room temperature with gentle agitation, 1 mg/ml peptide, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid	selective 13C and 15N		1 mg/mL
2	phosphate buffer	natural abundance		10 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 2LMN, Strand ID: A, B, C, D, E, F, G, H, I, J, K, L Detail

Release date

2012-01-04

Citation

Experimental constraints on quaternary structure in Alzheimer's beta-amyloid fibrils
Petkova, A., Yau, W., Tycko, R.
Biochemistry (2006), 45, 498-512, PubMed 16401079 , DOI 10.1021/bi051952q , Abstract

Related entities 1. 40-Residue Beta-Amyloid Fibril with Two-Fold Symmetry, : 1 : 97 : 5 : 10 : 19 entities Detail

Interaction partners 1. 40-Residue Beta-Amyloid Fibril with Two-Fold Symmetry, : 95 interactors Detail

More details for 95 interactors identified by 54 citations

Experiments performed 8 experiments Detail

1 2D fpRFDR

Instrument

Varian Infinity - 400 MHz

Sample

State solid, Solvent system 10 mM phosphate buffer, Pressure 1 atm, Temperature 300 K, pH 7.4, Details grown at room temperature with gentle agitation, 1 mg/ml peptide, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid	selective 13C and 15N		1 mg/mL
2	phosphate buffer	natural abundance		10 mM

2 2D RAD

Instrument

Varian Infinity - 400 MHz

Sample

State solid, Solvent system 10 mM phosphate buffer, Pressure 1 atm, Temperature 300 K, pH 7.4, Details grown at room temperature with gentle agitation, 1 mg/ml peptide, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid	selective 13C and 15N		1 mg/mL
2	phosphate buffer	natural abundance		10 mM

3 2D TEDOR

Instrument

Varian Infinity - 400 MHz

Sample

State solid, Solvent system 10 mM phosphate buffer, Pressure 1 atm, Temperature 300 K, pH 7.4, Details grown at room temperature with gentle agitation, 1 mg/ml peptide, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid	selective 13C and 15N		1 mg/mL
2	phosphate buffer	natural abundance		10 mM

4 fsREDOR

Instrument

Varian Infinity - 400 MHz

Sample

State solid, Solvent system 10 mM phosphate buffer, Pressure 1 atm, Temperature 300 K, pH 7.4, Details grown at room temperature with gentle agitation, 1 mg/ml peptide, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid	selective 13C and 15N		1 mg/mL
2	phosphate buffer	natural abundance		10 mM

5 15N-BARE

Instrument

Varian Infinity - 400 MHz

Sample

State solid, Solvent system 10 mM phosphate buffer, Pressure 1 atm, Temperature 300 K, pH 7.4, Details grown at room temperature with gentle agitation, 1 mg/ml peptide, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid	selective 13C and 15N		1 mg/mL
2	phosphate buffer	natural abundance		10 mM

6 13C-BARE

Instrument

Varian Infinity - 400 MHz

Sample

State solid, Solvent system 10 mM phosphate buffer, Pressure 1 atm, Temperature 300 K, pH 7.4, Details grown at room temperature with gentle agitation, 1 mg/ml peptide, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid	selective 13C and 15N		1 mg/mL
2	phosphate buffer	natural abundance		10 mM

7 PITHIRDS-CT

Instrument

Varian Infinity - 400 MHz

Sample

State solid, Solvent system 10 mM phosphate buffer, Pressure 1 atm, Temperature 300 K, pH 7.4, Details grown at room temperature with gentle agitation, 1 mg/ml peptide, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid	selective 13C and 15N		1 mg/mL
2	phosphate buffer	natural abundance		10 mM

8 2D NCACX

Instrument

Varian Infinity - 400 MHz

Sample

State solid, Solvent system 10 mM phosphate buffer, Pressure 1 atm, Temperature 300 K, pH 7.4, Details grown at room temperature with gentle agitation, 1 mg/ml peptide, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	beta-amyloid	selective 13C and 15N		1 mg/mL
2	phosphate buffer	natural abundance		10 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_18127_2lmn.nef
Input source #2: Coordindates	2lmn.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

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

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

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

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

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

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	40	0	0	100.0
B	B	40	0	0	100.0
C	C	40	0	0	100.0
D	D	40	0	0	100.0
E	E	40	0	0	100.0
F	F	40	0	0	100.0
G	G	40	0	0	100.0
H	H	40	0	0	100.0
I	I	40	0	0	100.0
J	J	40	0	0	100.0
K	K	40	0	0	100.0
L	L	40	0	0	100.0

Content subtype: combined_18127_2lmn.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	110		82.5 (chain: A, length: 40)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	542 (1)	undefined	55.0 (chain: A, length: 40), 65.0 (chain: B, length: 40), 65.0 (chain: C, length: 40), 57.5 (chain: D, length: 40), 62.5 (chain: E, length: 40), 65.0 (chain: F, length: 40), 65.0 (chain: G, length: 40), 65.0 (chain: H, length: 40), 57.5 (chain: I, length: 40), 55.0 (chain: J, length: 40), 62.5 (chain: K, length: 40), 65.0 (chain: L, length: 40)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	456 (456)	.	65.0 (chain: A, length: 40), 65.0 (chain: B, length: 40), 65.0 (chain: C, length: 40), 65.0 (chain: D, length: 40), 65.0 (chain: E, length: 40), 65.0 (chain: F, length: 40), 65.0 (chain: G, length: 40), 65.0 (chain: H, length: 40), 65.0 (chain: I, length: 40), 65.0 (chain: J, length: 40), 65.0 (chain: K, length: 40), 65.0 (chain: L, length: 40)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_2	Warning	184 (184)	.	37.5 (chain: A, length: 40), 37.5 (chain: B, length: 40), 37.5 (chain: C, length: 40), 37.5 (chain: D, length: 40), 37.5 (chain: E, length: 40), 37.5 (chain: F, length: 40), 37.5 (chain: G, length: 40), 37.5 (chain: H, length: 40), 37.5 (chain: I, length: 40), 37.5 (chain: J, length: 40), 37.5 (chain: K, length: 40), 37.5 (chain: L, length: 40)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 82.5%
- Total number of assignments
  - ¹³C chemical shifts: 93
  - ¹⁵N chemical shifts: 17
- Completeness of assignments
  - Entity_assemble_ID: A
- 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_4
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 55.0%
  - Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 65.0%
  - Entity_assembly_ID: C, Chain length: 40, Sequence coverage: 65.0%
  - Entity_assembly_ID: D, Chain length: 40, Sequence coverage: 57.5%
  - Entity_assembly_ID: E, Chain length: 40, Sequence coverage: 62.5%
  - Entity_assembly_ID: F, Chain length: 40, Sequence coverage: 65.0%
  - Entity_assembly_ID: G, Chain length: 40, Sequence coverage: 65.0%
  - Entity_assembly_ID: H, Chain length: 40, Sequence coverage: 65.0%
  - Entity_assembly_ID: I, Chain length: 40, Sequence coverage: 57.5%
  - Entity_assembly_ID: J, Chain length: 40, Sequence coverage: 55.0%
  - Entity_assembly_ID: K, Chain length: 40, Sequence coverage: 62.5%
  - Entity_assembly_ID: L, Chain length: 40, Sequence coverage: 65.0%
- Total number of restraints: 542
- Weight of restraints: 1.0 (542)
- Potential type of restraints: square-well-parabolic (542)
- Range of distance target values: 1.8, 4.65 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D
  - Chain_ID: E
  - Chain_ID: F
  - Chain_ID: G
  - Chain_ID: H
  - Chain_ID: I
  - Chain_ID: J
  - Chain_ID: K
  - Chain_ID: L
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 65.0%
  - Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 65.0%
  - Entity_assembly_ID: C, Chain length: 40, Sequence coverage: 65.0%
  - Entity_assembly_ID: D, Chain length: 40, Sequence coverage: 65.0%
  - Entity_assembly_ID: E, Chain length: 40, Sequence coverage: 65.0%
  - Entity_assembly_ID: F, Chain length: 40, Sequence coverage: 65.0%
  - Entity_assembly_ID: G, Chain length: 40, Sequence coverage: 65.0%
  - Entity_assembly_ID: H, Chain length: 40, Sequence coverage: 65.0%
  - Entity_assembly_ID: I, Chain length: 40, Sequence coverage: 65.0%
  - Entity_assembly_ID: J, Chain length: 40, Sequence coverage: 65.0%
  - Entity_assembly_ID: K, Chain length: 40, Sequence coverage: 65.0%
  - Entity_assembly_ID: L, Chain length: 40, Sequence coverage: 65.0%
- Total number of restraints: 456
- Total number of restraints per polymer type: 456
- Weight of restraints: 1.0 (456)
- Potential type of restraints: square-well-parabolic (456)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D
  - Chain_ID: E
  - Chain_ID: F
  - Chain_ID: G
  - Chain_ID: H
  - Chain_ID: I
  - Chain_ID: J
  - Chain_ID: K
  - Chain_ID: L

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_2
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 37.5%
  - Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 37.5%
  - Entity_assembly_ID: C, Chain length: 40, Sequence coverage: 37.5%
  - Entity_assembly_ID: D, Chain length: 40, Sequence coverage: 37.5%
  - Entity_assembly_ID: E, Chain length: 40, Sequence coverage: 37.5%
  - Entity_assembly_ID: F, Chain length: 40, Sequence coverage: 37.5%
  - Entity_assembly_ID: G, Chain length: 40, Sequence coverage: 37.5%
  - Entity_assembly_ID: H, Chain length: 40, Sequence coverage: 37.5%
  - Entity_assembly_ID: I, Chain length: 40, Sequence coverage: 37.5%
  - Entity_assembly_ID: J, Chain length: 40, Sequence coverage: 37.5%
  - Entity_assembly_ID: K, Chain length: 40, Sequence coverage: 37.5%
  - Entity_assembly_ID: L, Chain length: 40, Sequence coverage: 37.5%
- Total number of restraints: 184
- Potential type of restraints: undefined (184)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords Alzheimer's disease, amyloid, two-fold symmetry