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Found 1 Document (0.74 seconds)

BMRB: 18175

2LNQ

40-residue D23N beta amyloid fibril

Authors

Qiang, W., Yau, W., Luo, Y., Mattson, M.P., Tycko, R.

Assembly

40-residue D23N beta amyloid fibril

Entity

1. 40-residue D23N beta amyloid fibril (polymer, Thiol state: not present), 26 monomers, 2648.126 × 8 Da Detail

QKLVFFAENV GSNKGAIIGL MVGGVV

Total weight

21185.008 Da

Max. entity weight

2648.126 Da

Source organism

Homo sapiens

Exptl. method

NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 65.4 %, Completeness: 61.7 %, Completeness (bb): 68.5 % Detail

Polymer type: polypeptide(L)

	Total	¹³C
All	61.7 % (71 of 115)	61.7 % (71 of 115)
Backbone	68.5 % (50 of 73)	68.5 % (50 of 73)
Sidechain	60.3 % (38 of 63)	60.3 % (38 of 63)
Aromatic	0.0 % (0 of 10)	0.0 % (0 of 10)
Methyl	60.0 % (12 of 20)	60.0 % (12 of 20)

1. entity

QKLVFFAENV GSNKGAIIGL MVGGVV

Show sample condition

Sample

Solvent system H2O, Pressure 1 atm, Temperature 273 K, pH 7.4, Details amyloid fibril formed by 40-residue iowa mutant Abeta peptides

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C]		25 uM

Protein Blocks Logo

Calculated from 10 models in PDB: 2LNQ, Strand ID: A, B, C, D, E, F, G, H Detail

Release date

2012-02-05

Citation

Antiparallel β-sheet architecture in Iowa-mutant β-amyloid fibrils
Qiang, W., Yau, W., Luo, Y., Mattson, M.P., Tycko, R.
Proc. Natl. Acad. Sci. U. S. A. (2012), 109, 4443-4448, PubMed 22403062 , DOI 10.1073/pnas.1111305109 , Abstract

Related entities 1. 40-residue D23N beta amyloid fibril, : 1 : 1 : 88 : 16 entities Detail

Interaction partners 1. 40-residue D23N beta amyloid fibril, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 4 experiments Detail

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_18175_2lnq.nef
Input source #2: Coordindates	2lnq.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
DAEFRHDSGYEVHHQKLVFFAENVGSNKGAIIGLMVGGVV
||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAENVGSNKGAIIGLMVGGVV

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

--------10--------20--------30--------40
DAEFRHDSGYEVHHQKLVFFAENVGSNKGAIIGLMVGGVV
||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAENVGSNKGAIIGLMVGGVV

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

--------10--------20--------30--------40
DAEFRHDSGYEVHHQKLVFFAENVGSNKGAIIGLMVGGVV
||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAENVGSNKGAIIGLMVGGVV

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

--------10--------20--------30--------40
DAEFRHDSGYEVHHQKLVFFAENVGSNKGAIIGLMVGGVV
||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAENVGSNKGAIIGLMVGGVV

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

--------10--------20--------30--------40
DAEFRHDSGYEVHHQKLVFFAENVGSNKGAIIGLMVGGVV
||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAENVGSNKGAIIGLMVGGVV

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

--------10--------20--------30--------40
DAEFRHDSGYEVHHQKLVFFAENVGSNKGAIIGLMVGGVV
||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAENVGSNKGAIIGLMVGGVV

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

--------10--------20--------30--------40
DAEFRHDSGYEVHHQKLVFFAENVGSNKGAIIGLMVGGVV
||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAENVGSNKGAIIGLMVGGVV

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

--------10--------20--------30--------40
DAEFRHDSGYEVHHQKLVFFAENVGSNKGAIIGLMVGGVV
||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAENVGSNKGAIIGLMVGGVV

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

Content subtype: combined_18175_2lnq.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	74		42.5 (chain: A, length: 40)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	117 (1)	undefined	22.5 (chain: A, length: 40), 25.0 (chain: B, length: 40), 25.0 (chain: C, length: 40), 25.0 (chain: D, length: 40), 25.0 (chain: E, length: 40), 25.0 (chain: F, length: 40), 25.0 (chain: G, length: 40), 22.5 (chain: H, length: 40)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	35 (1)	undefined	12.5 (chain: A, length: 40), 15.0 (chain: B, length: 40), 15.0 (chain: C, length: 40), 15.0 (chain: D, length: 40), 15.0 (chain: E, length: 40), 15.0 (chain: F, length: 40), 15.0 (chain: G, length: 40), 12.5 (chain: H, length: 40)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	88 (1)	hbond	10.0 (chain: A, length: 40), 15.0 (chain: B, length: 40), 15.0 (chain: C, length: 40), 15.0 (chain: D, length: 40), 15.0 (chain: E, length: 40), 15.0 (chain: F, length: 40), 15.0 (chain: G, length: 40), 10.0 (chain: H, length: 40)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	256 (256)	.	55.0 (chain: A, length: 40), 55.0 (chain: B, length: 40), 55.0 (chain: C, length: 40), 55.0 (chain: D, length: 40), 55.0 (chain: E, length: 40), 55.0 (chain: F, length: 40), 55.0 (chain: G, length: 40), 55.0 (chain: H, length: 40)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_6	Warning	80 (80)	.	25.0 (chain: A, length: 40), 25.0 (chain: B, length: 40), 25.0 (chain: C, length: 40), 25.0 (chain: D, length: 40), 25.0 (chain: E, length: 40), 25.0 (chain: F, length: 40), 25.0 (chain: G, length: 40), 25.0 (chain: H, 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: 42.5%
- Total number of assignments
  - ¹³C chemical shifts: 74
- Completeness of assignments
- 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: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 22.5%
  - Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 25.0%
  - Entity_assembly_ID: C, Chain length: 40, Sequence coverage: 25.0%
  - Entity_assembly_ID: D, Chain length: 40, Sequence coverage: 25.0%
  - Entity_assembly_ID: E, Chain length: 40, Sequence coverage: 25.0%
  - Entity_assembly_ID: F, Chain length: 40, Sequence coverage: 25.0%
  - Entity_assembly_ID: G, Chain length: 40, Sequence coverage: 25.0%
  - Entity_assembly_ID: H, Chain length: 40, Sequence coverage: 22.5%
- Total number of restraints: 117
- Weight of restraints: 1.0 (117)
- Potential type of restraints: square-well-parabolic (117)
- Range of distance target values: 4.5, 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
- Distance restraints on contact map
- 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: 12.5%
    - Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 15.0%
    - Entity_assembly_ID: C, Chain length: 40, Sequence coverage: 15.0%
    - Entity_assembly_ID: D, Chain length: 40, Sequence coverage: 15.0%
    - Entity_assembly_ID: E, Chain length: 40, Sequence coverage: 15.0%
    - Entity_assembly_ID: F, Chain length: 40, Sequence coverage: 15.0%
    - Entity_assembly_ID: G, Chain length: 40, Sequence coverage: 15.0%
    - Entity_assembly_ID: H, Chain length: 40, Sequence coverage: 12.5%
  - Total number of restraints: 35
  - Weight of restraints: 1.0 (35)
  - Potential type of restraints: square-well-parabolic (35)
  - Range of distance target values: 5.0, 5.2 (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
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_3
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 10.0%
      - Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 15.0%
      - Entity_assembly_ID: C, Chain length: 40, Sequence coverage: 15.0%
      - Entity_assembly_ID: D, Chain length: 40, Sequence coverage: 15.0%
      - Entity_assembly_ID: E, Chain length: 40, Sequence coverage: 15.0%
      - Entity_assembly_ID: F, Chain length: 40, Sequence coverage: 15.0%
      - Entity_assembly_ID: G, Chain length: 40, Sequence coverage: 15.0%
      - Entity_assembly_ID: H, Chain length: 40, Sequence coverage: 10.0%
    - Total number of restraints: 88
    - Weight of restraints: 1.0 (88)
    - Potential type of restraints: square-well-parabolic (88)
    - Range of distance target values: 1.6, 2.6 (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
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: OK
- Experiment type: .
- 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: 55.0%
  - Entity_assembly_ID: C, Chain length: 40, Sequence coverage: 55.0%
  - Entity_assembly_ID: D, Chain length: 40, Sequence coverage: 55.0%
  - Entity_assembly_ID: E, Chain length: 40, Sequence coverage: 55.0%
  - Entity_assembly_ID: F, Chain length: 40, Sequence coverage: 55.0%
  - Entity_assembly_ID: G, Chain length: 40, Sequence coverage: 55.0%
  - Entity_assembly_ID: H, Chain length: 40, Sequence coverage: 55.0%
- Total number of restraints: 256
- Total number of restraints per polymer type: 256
- Weight of restraints: 1.0 (256)
- Potential type of restraints: square-well-parabolic (256)
- 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

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_6
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 25.0%
  - Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 25.0%
  - Entity_assembly_ID: C, Chain length: 40, Sequence coverage: 25.0%
  - Entity_assembly_ID: D, Chain length: 40, Sequence coverage: 25.0%
  - Entity_assembly_ID: E, Chain length: 40, Sequence coverage: 25.0%
  - Entity_assembly_ID: F, Chain length: 40, Sequence coverage: 25.0%
  - Entity_assembly_ID: G, Chain length: 40, Sequence coverage: 25.0%
  - Entity_assembly_ID: H, Chain length: 40, Sequence coverage: 25.0%
- Total number of restraints: 80
- Potential type of restraints: undefined (80)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords amyloid fibril, antiparallel beta sheet, Iowa mutant

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Found 1 Document (0.74 seconds)

BMRB: 18175

Sample

Related entities 1. 40-residue D23N beta amyloid fibril, : 1 : 1 : 88 : 16 entities Detail

Interaction partners 1. 40-residue D23N beta amyloid fibril, : 2 interactors Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail