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Found 1 Document (3.025 seconds)

BMRB: 18131

2LMQ

Structural Model for a 40-residue Beta-Amyloid Fibril with Three-Fold Symmetry, Negative Stagger

Authors

Tycko, R., Paravastu, A.

Assembly

40-residue Beta-Amyloid Fibril with Three-Fold Symmetry, Negative Stagger

Entity

1. 40-residue Beta-Amyloid Fibril with Three-Fold Symmetry, Negative Stagger (polymer, Thiol state: not present), 40 monomers, 4329.801 × 18 Da Detail

DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV

Total weight

77936.414 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: 80.0 %, Completeness: 52.0 %, Completeness (bb): 78.9 % Detail

Polymer type: polypeptide(L)

	Total	¹³C
All	52.0 % (92 of 177)	52.0 % (92 of 177)
Backbone	78.9 % (90 of 114)	78.9 % (90 of 114)
Sidechain	28.9 % (28 of 97)	28.9 % (28 of 97)
Aromatic	0.0 % (0 of 25)	0.0 % (0 of 25)
Methyl	17.4 % (4 of 23)	17.4 % (4 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 quiescently at room temperature, 1 mg/ml peptide, pH 7.4. Structurally purified by multiple rounds of seeded growth.

#	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: 2LMQ, Strand ID: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R Detail

Release date

2012-01-04

Citation

Experimental constraints on quaternary structure in Alzheimer's beta-amyloid fibrils
Paravastu, A., Leapman, R., 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 Three-Fold Symmetry, Negative Stagger, : 1 : 90 : 5 : 7 : 17 entities Detail

Interaction partners 1. 40-residue Beta-Amyloid Fibril with Three-Fold Symmetry, Negative Stagger, : 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 quiescently at room temperature, 1 mg/ml peptide, pH 7.4. Structurally purified by multiple rounds of seeded growth.

#	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

#	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

#	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

#	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

#	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

#	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

#	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

#	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_18131_2lmq.nef
Input source #2: Coordindates	2lmq.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

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

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

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

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

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

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

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

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

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

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

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

--------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
J	J	40	100.0
K	K	40	100.0
L	L	40	100.0
M	M	40	100.0
A	A	40	100.0
A	A	40	100.0
A	A	40	100.0
A	A	40	100.0
A	A	40	100.0

Content subtype: combined_18131_2lmq.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	90		80.0 (chain: A, length: 40)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	951 (1)	undefined	50.0 (chain: A, length: 40), 60.0 (chain: B, length: 40), 57.5 (chain: C, length: 40), 55.0 (chain: D, length: 40), 50.0 (chain: E, length: 40), 57.5 (chain: F, length: 40), 60.0 (chain: G, length: 40), 60.0 (chain: H, length: 40), 57.5 (chain: I, length: 40), 55.0 (chain: J, length: 40), 57.5 (chain: K, length: 40), 60.0 (chain: L, length: 40), 60.0 (chain: M, length: 40), 57.5 (chain: N, length: 40), 55.0 (chain: O, length: 40), 50.0 (chain: P, length: 40), 57.5 (chain: Q, length: 40), 60.0 (chain: R, length: 40)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	720 (720)	.	67.5 (chain: A, length: 40), 67.5 (chain: B, length: 40), 67.5 (chain: C, length: 40), 67.5 (chain: D, length: 40), 67.5 (chain: E, length: 40), 67.5 (chain: F, length: 40), 67.5 (chain: G, length: 40), 67.5 (chain: H, length: 40), 67.5 (chain: I, length: 40), 67.5 (chain: J, length: 40), 67.5 (chain: K, length: 40), 67.5 (chain: L, length: 40), 67.5 (chain: M, length: 40), 67.5 (chain: N, length: 40), 67.5 (chain: O, length: 40), 67.5 (chain: P, length: 40), 67.5 (chain: Q, length: 40), 67.5 (chain: R, length: 40)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_3	Warning	306 (306)	.	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), 37.5 (chain: M, length: 40), 37.5 (chain: N, length: 40), 37.5 (chain: O, length: 40), 37.5 (chain: P, length: 40), 37.5 (chain: Q, length: 40), 37.5 (chain: R, 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: 80.0%
- Total number of assignments
  - ¹³C chemical shifts: 90
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	177	90	50.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	80	64	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	97	26	26.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	24	2	8.3

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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 50.0%
  - Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 60.0%
  - Entity_assembly_ID: C, Chain length: 40, Sequence coverage: 57.5%
  - Entity_assembly_ID: D, Chain length: 40, Sequence coverage: 55.0%
  - Entity_assembly_ID: E, Chain length: 40, Sequence coverage: 50.0%
  - Entity_assembly_ID: F, Chain length: 40, Sequence coverage: 57.5%
  - Entity_assembly_ID: G, Chain length: 40, Sequence coverage: 60.0%
  - Entity_assembly_ID: H, Chain length: 40, Sequence coverage: 60.0%
  - 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: 57.5%
  - Entity_assembly_ID: L, Chain length: 40, Sequence coverage: 60.0%
  - Entity_assembly_ID: M, Chain length: 40, Sequence coverage: 60.0%
  - Entity_assembly_ID: N, Chain length: 40, Sequence coverage: 57.5%
  - Entity_assembly_ID: O, Chain length: 40, Sequence coverage: 55.0%
  - Entity_assembly_ID: P, Chain length: 40, Sequence coverage: 50.0%
  - Entity_assembly_ID: Q, Chain length: 40, Sequence coverage: 57.5%
  - Entity_assembly_ID: R, Chain length: 40, Sequence coverage: 60.0%
- Total number of restraints: 951
- Weight of restraints: 1.0 (951)
- Potential type of restraints: square-well-parabolic (951)
- Range of distance target values: 1.8, 6.0 (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
  - Chain_ID: M
  - Chain_ID: N
  - Chain_ID: O
  - Chain_ID: P
  - Chain_ID: Q
  - Chain_ID: R
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 67.5%
  - Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 67.5%
  - Entity_assembly_ID: C, Chain length: 40, Sequence coverage: 67.5%
  - Entity_assembly_ID: D, Chain length: 40, Sequence coverage: 67.5%
  - Entity_assembly_ID: E, Chain length: 40, Sequence coverage: 67.5%
  - Entity_assembly_ID: F, Chain length: 40, Sequence coverage: 67.5%
  - Entity_assembly_ID: G, Chain length: 40, Sequence coverage: 67.5%
  - Entity_assembly_ID: H, Chain length: 40, Sequence coverage: 67.5%
  - Entity_assembly_ID: I, Chain length: 40, Sequence coverage: 67.5%
  - Entity_assembly_ID: J, Chain length: 40, Sequence coverage: 67.5%
  - Entity_assembly_ID: K, Chain length: 40, Sequence coverage: 67.5%
  - Entity_assembly_ID: L, Chain length: 40, Sequence coverage: 67.5%
  - Entity_assembly_ID: M, Chain length: 40, Sequence coverage: 67.5%
  - Entity_assembly_ID: N, Chain length: 40, Sequence coverage: 67.5%
  - Entity_assembly_ID: O, Chain length: 40, Sequence coverage: 67.5%
  - Entity_assembly_ID: P, Chain length: 40, Sequence coverage: 67.5%
  - Entity_assembly_ID: Q, Chain length: 40, Sequence coverage: 67.5%
  - Entity_assembly_ID: R, Chain length: 40, Sequence coverage: 67.5%
- Total number of restraints: 720
- Total number of restraints per polymer type: 720
- Weight of restraints: 1.0 (720)
- Potential type of restraints: square-well-parabolic (720)
- 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
  - Chain_ID: M
  - Chain_ID: N
  - Chain_ID: O
  - Chain_ID: P
  - Chain_ID: Q
  - Chain_ID: R

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_3
- 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%
  - Entity_assembly_ID: M, Chain length: 40, Sequence coverage: 37.5%
  - Entity_assembly_ID: N, Chain length: 40, Sequence coverage: 37.5%
  - Entity_assembly_ID: O, Chain length: 40, Sequence coverage: 37.5%
  - Entity_assembly_ID: P, Chain length: 40, Sequence coverage: 37.5%
  - Entity_assembly_ID: Q, Chain length: 40, Sequence coverage: 37.5%
  - Entity_assembly_ID: R, Chain length: 40, Sequence coverage: 37.5%
- Total number of restraints: 306
- Potential type of restraints: undefined (306)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

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

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Found 1 Document (3.025 seconds)

BMRB: 18131

Sample

Related entities 1. 40-residue Beta-Amyloid Fibril with Three-Fold Symmetry, Negative Stagger, : 1 : 90 : 5 : 7 : 17 entities Detail

Interaction partners 1. 40-residue Beta-Amyloid Fibril with Three-Fold Symmetry, Negative Stagger, : 95 interactors Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 5 contents Detail