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Found 1 Document (3.48 seconds)

BMRB: 25289

2MVX

Atomic-resolution 3D structure of amyloid-beta fibrils: the Osaka mutation

Authors

Schuetz, A.K., Vagt, T., Huber, M., Ovchinnikova, O.Y., Cadalbert, R., Wall, J., Guentert, P., Bockmann, A., Glockshuber, R., Meier, B.H.

Assembly

amyloid-beta fibrils: the Osaka mutation

Entity

1. amyloid-beta fibrils: the Osaka mutation (polymer, Thiol state: not present), 39 monomers, 4200.688 × 10 Da Detail

DAEFRHDSGY EVHHQKLVFF ADVGSNKGAI IGLMVGGVV

Total weight

42006.88 Da

Max. entity weight

4200.688 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 100.0 %, Completeness: 94.4 %, Completeness (bb): 98.7 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	94.4 % (202 of 214)	93.1 % (161 of 173)	100.0 % (41 of 41)
Backbone	98.7 % (148 of 150)	98.2 % (109 of 111)	100.0 % (39 of 39)
Sidechain	89.7 % (87 of 97)	89.5 % (85 of 95)	100.0 % (2 of 2)
Aromatic	68.0 % (17 of 25)	68.0 % (17 of 25)
Methyl	91.3 % (21 of 23)	91.3 % (21 of 23)

1. amyloid beta

DAEFRHDSGY EVHHQKLVFF ADVGSNKGAI IGLMVGGVV

Show sample condition

Sample #1

Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	amyloid beta	[U-100% 13C; U-100% 15N]		15 mg

Sample #2

Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
2	amyloid beta	[U-100% 13C]		15 mg

Sample #3

Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7, Details Selectively 13C and 15N labeled monomers were mixed before fibrillation in a 1/1 ratio.

#	Name	Isotope labeling	Type	Concentration
3	amyloid beta	[U-100% 13C; U-100% 15N]		15 mg

Sample #4

Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	amyloid beta	[U-100% 2-13C-glucose; U-100% 15N]		15 mg

Sample #5

Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7, Details Selectively [13C,15N} and natural abundance monomers were mixed before fibrillation in a 1/4 ratio.

#	Name	Isotope labeling	Type	Concentration
5	amyloid beta	[U-100% 13C; U-100% 15N]/natural abundance		15 mg

Chem. Shift Complete2

Sequence coverage: 100.0 %, Completeness: 86.4 %, Completeness (bb): 88.0 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	86.4 % (370 of 428)	93.1 % (322 of 346)	58.5 % (48 of 82)
Backbone	88.0 % (264 of 300)	98.2 % (218 of 222)	59.0 % (46 of 78)
Sidechain	88.7 % (172 of 194)	89.5 % (170 of 190)	50.0 % (2 of 4)
Aromatic	68.0 % (34 of 50)	68.0 % (34 of 50)
Methyl	91.3 % (42 of 46)	91.3 % (42 of 46)

1. amyloid beta

DAEFRHDSGY EVHHQKLVFF ADVGSNKGAI IGLMVGGVV

Show sample condition

Sample #1

Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	amyloid beta	[U-100% 13C; U-100% 15N]		15 mg

Sample #2

Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
2	amyloid beta	[U-100% 13C]		15 mg

Sample #3

Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7, Details Selectively 13C and 15N labeled monomers were mixed before fibrillation in a 1/1 ratio.

#	Name	Isotope labeling	Type	Concentration
3	amyloid beta	[U-100% 13C; U-100% 15N]		15 mg

Sample #4

Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	amyloid beta	[U-100% 2-13C-glucose; U-100% 15N]		15 mg

Sample #5

Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7, Details Selectively [13C,15N} and natural abundance monomers were mixed before fibrillation in a 1/4 ratio.

#	Name	Isotope labeling	Type	Concentration
5	amyloid beta	[U-100% 13C; U-100% 15N]/natural abundance		15 mg

Chem. Shift Complete3

Sequence coverage: 97.4 %, Completeness: 82.7 %, Completeness (bb): 86.0 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	82.7 % (531 of 642)	85.5 % (444 of 519)	70.7 % (87 of 123)
Backbone	86.0 % (387 of 450)	91.3 % (304 of 333)	70.9 % (83 of 117)
Sidechain	79.7 % (232 of 291)	80.0 % (228 of 285)	66.7 % (4 of 6)
Aromatic	60.0 % (45 of 75)	60.0 % (45 of 75)
Methyl	76.8 % (53 of 69)	76.8 % (53 of 69)

1. amyloid beta

DAEFRHDSGY EVHHQKLVFF ADVGSNKGAI IGLMVGGVV

Show sample condition

Sample #1

Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	amyloid beta	[U-100% 13C; U-100% 15N]		15 mg

Sample #2

Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
2	amyloid beta	[U-100% 13C]		15 mg

Sample #3

Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7, Details Selectively 13C and 15N labeled monomers were mixed before fibrillation in a 1/1 ratio.

#	Name	Isotope labeling	Type	Concentration
3	amyloid beta	[U-100% 13C; U-100% 15N]		15 mg

Sample #4

Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	amyloid beta	[U-100% 2-13C-glucose; U-100% 15N]		15 mg

Sample #5

Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7, Details Selectively [13C,15N} and natural abundance monomers were mixed before fibrillation in a 1/4 ratio.

#	Name	Isotope labeling	Type	Concentration
5	amyloid beta	[U-100% 13C; U-100% 15N]/natural abundance		15 mg

Protein Blocks Logo

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

Release date

2015-08-24

Citation

Atomic-resolution three-dimensional structure of amyloid β fibrils bearing the Osaka mutation
Schuetz, A.K., Vagt, T., Huber, M., Ovchinnikova, O.Y., Cadalbert, R., Wall, J., Guentert, P., Bockmann, A., Glockshuber, R., Meier, B.H.
Angew. Chem Int Ed Engl. (2015), 54, 331-335, PubMed 25395337 , DOI 10.1002/anie.201408598 , Abstract

Related entities 1. amyloid-beta fibrils: the Osaka mutation, : 1 : 116 entities Detail

Sample

#	Name	Isotope labeling	Type	Concentration
5	amyloid beta	[U-100% 13C; U-100% 15N]/natural abundance		15 mg

10 CHHC 500 us

Instrument

Bruker Avance - 850 MHz widebore magnet Bruker triple resonance 3.2 mm MAS probe

Sample

State solid, Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
2	amyloid beta	[U-100% 13C]		15 mg

11 CHHC 500 us

Instrument

Bruker Avance - 850 MHz widebore magnet Bruker triple resonance 3.2 mm MAS probe

Sample

#	Name	Isotope labeling	Type	Concentration
5	amyloid beta	[U-100% 13C; U-100% 15N]/natural abundance		15 mg

12 PDSD 4 s

Instrument

Bruker Avance - 850 MHz widebore magnet Bruker triple resonance 3.2 mm MAS probe

Sample

State solid, Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	amyloid beta	[U-100% 2-13C-glucose; U-100% 15N]		15 mg

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25289_2mvx.nef
Input source #2: Coordindates	2mvx.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	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	22	.	Not matched with CCD	None
B	22	.	Not matched with CCD	None
C	22	.	Not matched with CCD	None
D	22	.	Not matched with CCD	None
E	22	.	Not matched with CCD	None
F	22	.	Not matched with CCD	None
G	22	.	Not matched with CCD	None
H	22	.	Not matched with CCD	None
I	22	.	Not matched with CCD	None
J	22	.	Not matched with CCD	None

Sequence alignments

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

--3                                     
.DA                                     
 ||                                     
-DAEFRHDSGYEVHHQKLVFFADVGSNKGAIIGLMVGGVV
 ---------10--------20--------30--------

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

--3                                     
.DA                                     
 ||                                     
-DAEFRHDSGYEVHHQKLVFFADVGSNKGAIIGLMVGGVV
 ---------10--------20--------30--------

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

--3                                     
.DA                                     
 ||                                     
-DAEFRHDSGYEVHHQKLVFFADVGSNKGAIIGLMVGGVV
 ---------10--------20--------30--------

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

--3                                     
.DA                                     
 ||                                     
-DAEFRHDSGYEVHHQKLVFFADVGSNKGAIIGLMVGGVV
 ---------10--------20--------30--------

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

--3                                     
.DA                                     
 ||                                     
-DAEFRHDSGYEVHHQKLVFFADVGSNKGAIIGLMVGGVV
 ---------10--------20--------30--------

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

--3                                     
.DA                                     
 ||                                     
-DAEFRHDSGYEVHHQKLVFFADVGSNKGAIIGLMVGGVV
 ---------10--------20--------30--------

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

--3                                     
.DA                                     
 ||                                     
-DAEFRHDSGYEVHHQKLVFFADVGSNKGAIIGLMVGGVV
 ---------10--------20--------30--------

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

--3                                     
.DA                                     
 ||                                     
-DAEFRHDSGYEVHHQKLVFFADVGSNKGAIIGLMVGGVV
 ---------10--------20--------30--------

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

--3                                     
.DA                                     
 ||                                     
-DAEFRHDSGYEVHHQKLVFFADVGSNKGAIIGLMVGGVV
 ---------10--------20--------30--------

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

--3                                     
.DA                                     
 ||                                     
-DAEFRHDSGYEVHHQKLVFFADVGSNKGAIIGLMVGGVV
 ---------10--------20--------30--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Sequence coverage (%)
A	A	39	1	100.0
B	B	39	1	100.0
C	C	39	1	100.0
D	D	39	1	100.0
E	E	39	1	100.0
F	F	39	1	100.0
G	G	39	1	100.0
H	H	39	1	100.0
I	I	39	1	100.0
J	J	39	1	100.0

Content subtype: combined_25289_2mvx.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shift_uniform_13C15N	Error	201		90.0 (chain: A, length: 40)
2	Assigned chemical shifts	assigned_chemical_shift_uniform_13C	Error	159		90.0 (chain: A, length: 40)
3	Assigned chemical shifts	assigned_chemical_shift_2-13C-glucose	Error	153		87.5 (chain: A, length: 40)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	Error	14147 (1)	undefined	97.5 (chain: A, length: 40), 97.5 (chain: B, length: 40), 97.5 (chain: C, length: 40), 97.5 (chain: D, length: 40), 97.5 (chain: E, length: 40), 97.5 (chain: F, length: 40), 97.5 (chain: G, length: 40), 97.5 (chain: H, length: 40), 97.5 (chain: I, length: 40), 97.5 (chain: J, length: 40)
2	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	76 (1)	hbond	25.0 (chain: A, length: 40), 30.0 (chain: C, length: 40)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	56 (56)	.	95.0 (chain: A, length: 40)

Assigned chemical shifts

Saveframe: assigned_chemical_shift_uniform_13C15N
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 90.0%
- Total number of assignments
  - ¹³C chemical shifts: 158
  - ¹⁵N chemical shifts: 43
- 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
Saveframe: assigned_chemical_shift_uniform_13C
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 90.0%
- Total number of assignments
  - ¹³C chemical shifts: 159
- 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
Saveframe: assigned_chemical_shift_2-13C-glucose
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 87.5%
- Total number of assignments
  - ¹³C chemical shifts: 114
  - ¹⁵N chemical shifts: 39
- 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: DYANA/DIANA_distance_constraints_4
- Status: Error
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 97.5%
  - Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 97.5%
  - Entity_assembly_ID: C, Chain length: 40, Sequence coverage: 97.5%
  - Entity_assembly_ID: D, Chain length: 40, Sequence coverage: 97.5%
  - Entity_assembly_ID: E, Chain length: 40, Sequence coverage: 97.5%
  - Entity_assembly_ID: F, Chain length: 40, Sequence coverage: 97.5%
  - Entity_assembly_ID: G, Chain length: 40, Sequence coverage: 97.5%
  - Entity_assembly_ID: H, Chain length: 40, Sequence coverage: 97.5%
  - Entity_assembly_ID: I, Chain length: 40, Sequence coverage: 97.5%
  - Entity_assembly_ID: J, Chain length: 40, Sequence coverage: 97.5%
- Total number of restraints: 14081
- Weight of restraints: 1.0 (14081)
- Potential type of restraints: upper-bound-parabolic (14081)
- Range of distance target values: 0.0, 10.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in 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
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_2
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 25.0%
    - Entity_assembly_ID: C, Chain length: 40, Sequence coverage: 30.0%
  - Total number of restraints: 76
  - Weight of restraints: 1.0 (76)
  - Potential type of restraints: upper-bound-parabolic (76)
  - Range of distance target values: 1.8, 3.0 (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
    - Chain_ID: D
      None
    - Chain_ID: E
      None
    - Chain_ID: F
      None
    - Chain_ID: G
      None
    - Chain_ID: H
      None
    - Chain_ID: I
      None
    - Chain_ID: J
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 95.0%
- Total number of restraints: 56
- Total number of restraints per polymer type: 56
- Weight of restraints: 1.0 (56)
- Potential type of restraints: square-well-parabolic (56)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords Osaka mutation, amyloid beta, amyloid fibrils, solid-state NMR

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Found 1 Document (3.48 seconds)

BMRB: 25289

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Related entities 1. amyloid-beta fibrils: the Osaka mutation, : 1 : 116 entities Detail

Interaction partners 1. amyloid-beta fibrils: the Osaka mutation, : 95 interactors Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 7 contents Detail