BMRBj - BMREntryMaster

Found 1 Document (0.712 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

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.712 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