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Found 1 Document (3.005 seconds)

BMRB: 25429

2MXU

42-Residue Beta Amyloid Fibril

Authors

Xiao, Y., Ma, B., McElheny, D., Parthasarathy, S., Long, F., Hoshi, M., Nussinov, R., Ishii, Y.

Assembly

42-Residue Beta Amyloid Fibril

Entity

1. 42-Residue Beta Amyloid Fibril (polymer, Thiol state: not present), 42 monomers, 4514.037 × 12 Da Detail

DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV IA

Total weight

54168.445 Da

Max. entity weight

4514.037 Da

Source organism

Homo sapiens

Exptl. method

NMR

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 66.7 %, Completeness: 47.4 %, Completeness (bb): 63.6 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	47.4 % (109 of 230)	45.2 % (84 of 186)	56.8 % (25 of 44)
Backbone	63.6 % (103 of 162)	65.0 % (78 of 120)	59.5 % (25 of 42)
Sidechain	26.9 % (28 of 104)	27.5 % (28 of 102)	0.0 % (0 of 2)
Aromatic	0.0 % (0 of 25)	0.0 % (0 of 25)
Methyl	30.8 % (8 of 26)	30.8 % (8 of 26)

1. entity

DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV IA

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 (±1) K, pH 7.4 (±0.1)

#	Name	Isotope labeling	Concentration
1	AB42	[U-100% 13C; U-100% 15N]	50 uM
2	sodium phosphate	natural abundance	10 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

Protein Blocks Logo

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

Release date

2015-05-03

Citation

Aβ(1-42) fibril structure illuminates self-recognition and replication of amyloid in Alzheimer's disease
Xiao, Y., Ma, B., McElheny, D., Parthasarathy, S., Long, F., Hoshi, M., Nussinov, R., Ishii, Y.
Nat. Struct. Mol. Biol. (2015), 22, 499-505, PubMed 25938662 , DOI 10.1038/nsmb.2991 , Abstract

Related entities 1. 42-Residue Beta Amyloid Fibril, : 1 : 44 : 3 : 54 : 18 entities Detail

Interaction partners 1. 42-Residue Beta Amyloid Fibril, : 96 interactors Detail

More details for 96 interactors identified by 55 citations

Experiments performed 5 experiments Detail

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25429_2mxu.nef
Input source #2: Coordindates	2mxu.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--
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA
||||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA

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

--------10--------20--------30--------40--
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA
||||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA

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

--------10--------20--------30--------40--
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA
||||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA

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

--------10--------20--------30--------40--
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA
||||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA

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

--------10--------20--------30--------40--
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA
||||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA

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

--------10--------20--------30--------40--
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA
||||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA

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

--------10--------20--------30--------40--
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA
||||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA

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

--------10--------20--------30--------40--
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA
||||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA

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

--------10--------20--------30--------40--
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA
||||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA

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

--------10--------20--------30--------40--
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA
||||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA

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

--------10--------20--------30--------40--
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA
||||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA

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

--------10--------20--------30--------40--
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA
||||||||||||||||||||||||||||||||||||||||||
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	42	100.0
B	B	42	100.0
C	C	42	100.0
D	D	42	100.0
E	E	42	100.0
F	F	42	100.0
G	G	42	100.0
H	H	42	100.0
I	I	42	100.0
J	J	42	100.0
K	K	42	100.0
L	L	42	100.0

Content subtype: combined_25429_2mxu.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	103		66.7 (chain: A, length: 42)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	4017 (1)	undefined	76.2 (chain: A, length: 42), 76.2 (chain: B, length: 42), 76.2 (chain: C, length: 42), 76.2 (chain: D, length: 42), 76.2 (chain: E, length: 42), 76.2 (chain: F, length: 42), 76.2 (chain: G, length: 42), 76.2 (chain: H, length: 42), 76.2 (chain: I, length: 42), 76.2 (chain: J, length: 42), 76.2 (chain: K, length: 42), 76.2 (chain: L, length: 42)
2	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	455 (1)	undefined	19.0 (chain: A, length: 42), 19.0 (chain: B, length: 42), 19.0 (chain: C, length: 42), 19.0 (chain: D, length: 42), 19.0 (chain: E, length: 42), 19.0 (chain: F, length: 42), 19.0 (chain: G, length: 42), 19.0 (chain: H, length: 42), 19.0 (chain: I, length: 42), 19.0 (chain: J, length: 42), 19.0 (chain: K, length: 42), 19.0 (chain: L, length: 42)
3	Distance restraints	DYANA/DIANA_distance_constraints_7	Warning	3344 (1)	undefined	76.2 (chain: A, length: 42), 76.2 (chain: B, length: 42), 76.2 (chain: C, length: 42), 76.2 (chain: D, length: 42), 76.2 (chain: E, length: 42), 76.2 (chain: F, length: 42), 76.2 (chain: G, length: 42), 76.2 (chain: H, length: 42), 76.2 (chain: I, length: 42), 76.2 (chain: J, length: 42), 76.2 (chain: K, length: 42), 76.2 (chain: L, length: 42)
4	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	176 (1)	hbond	9.5 (chain: A, length: 42), 26.2 (chain: B, length: 42), 26.2 (chain: C, length: 42), 16.7 (chain: D, length: 42), 26.2 (chain: E, length: 42), 26.2 (chain: F, length: 42), 26.2 (chain: G, length: 42), 26.2 (chain: H, length: 42), 26.2 (chain: I, length: 42), 26.2 (chain: J, length: 42), 26.2 (chain: K, length: 42), 26.2 (chain: L, length: 42)
5	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	176 (1)	hbond	9.5 (chain: A, length: 42), 26.2 (chain: B, length: 42), 26.2 (chain: C, length: 42), 16.7 (chain: D, length: 42), 26.2 (chain: E, length: 42), 26.2 (chain: F, length: 42), 26.2 (chain: G, length: 42), 26.2 (chain: H, length: 42), 26.2 (chain: I, length: 42), 26.2 (chain: J, length: 42), 26.2 (chain: K, length: 42), 26.2 (chain: L, length: 42)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 42, Sequence coverage: 66.7%
- Total number of assignments
  - ¹³C chemical shifts: 78
  - ¹⁵N chemical shifts: 25
- 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	186	78	41.9
¹⁵N chemical shifts	45	25	55.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	84	56	66.7
¹⁵N chemical shifts	42	25	59.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	102	22	21.6
¹⁵N chemical shifts	3	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	27	4	14.8

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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_4
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 42, Sequence coverage: 76.2%
  - Entity_assembly_ID: B, Chain length: 42, Sequence coverage: 76.2%
  - Entity_assembly_ID: C, Chain length: 42, Sequence coverage: 76.2%
  - Entity_assembly_ID: D, Chain length: 42, Sequence coverage: 76.2%
  - Entity_assembly_ID: E, Chain length: 42, Sequence coverage: 76.2%
  - Entity_assembly_ID: F, Chain length: 42, Sequence coverage: 76.2%
  - Entity_assembly_ID: G, Chain length: 42, Sequence coverage: 76.2%
  - Entity_assembly_ID: H, Chain length: 42, Sequence coverage: 76.2%
  - Entity_assembly_ID: I, Chain length: 42, Sequence coverage: 76.2%
  - Entity_assembly_ID: J, Chain length: 42, Sequence coverage: 76.2%
  - Entity_assembly_ID: K, Chain length: 42, Sequence coverage: 76.2%
  - Entity_assembly_ID: L, Chain length: 42, Sequence coverage: 76.2%
- Total number of restraints: 4017
- Weight of restraints: 1.0 (4017)
- Potential type of restraints: upper-bound-parabolic (4017)
- Range of distance target values: 3.9, 6.5 (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
- Saveframe: DYANA/DIANA_distance_constraints_5
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 42, Sequence coverage: 19.0%
    - Entity_assembly_ID: B, Chain length: 42, Sequence coverage: 19.0%
    - Entity_assembly_ID: C, Chain length: 42, Sequence coverage: 19.0%
    - Entity_assembly_ID: D, Chain length: 42, Sequence coverage: 19.0%
    - Entity_assembly_ID: E, Chain length: 42, Sequence coverage: 19.0%
    - Entity_assembly_ID: F, Chain length: 42, Sequence coverage: 19.0%
    - Entity_assembly_ID: G, Chain length: 42, Sequence coverage: 19.0%
    - Entity_assembly_ID: H, Chain length: 42, Sequence coverage: 19.0%
    - Entity_assembly_ID: I, Chain length: 42, Sequence coverage: 19.0%
    - Entity_assembly_ID: J, Chain length: 42, Sequence coverage: 19.0%
    - Entity_assembly_ID: K, Chain length: 42, Sequence coverage: 19.0%
    - Entity_assembly_ID: L, Chain length: 42, Sequence coverage: 19.0%
  - Total number of restraints: 455
  - Weight of restraints: 1.0 (455)
  - Potential type of restraints: upper-bound-parabolic (455)
  - Range of distance target values: 3.9, 6.5 (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
    - Chain_ID: K
    - Chain_ID: L
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_7
    - Status: Warning
    - Experiment type: undefined
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 42, Sequence coverage: 76.2%
      - Entity_assembly_ID: B, Chain length: 42, Sequence coverage: 76.2%
      - Entity_assembly_ID: C, Chain length: 42, Sequence coverage: 76.2%
      - Entity_assembly_ID: D, Chain length: 42, Sequence coverage: 76.2%
      - Entity_assembly_ID: E, Chain length: 42, Sequence coverage: 76.2%
      - Entity_assembly_ID: F, Chain length: 42, Sequence coverage: 76.2%
      - Entity_assembly_ID: G, Chain length: 42, Sequence coverage: 76.2%
      - Entity_assembly_ID: H, Chain length: 42, Sequence coverage: 76.2%
      - Entity_assembly_ID: I, Chain length: 42, Sequence coverage: 76.2%
      - Entity_assembly_ID: J, Chain length: 42, Sequence coverage: 76.2%
      - Entity_assembly_ID: K, Chain length: 42, Sequence coverage: 76.2%
      - Entity_assembly_ID: L, Chain length: 42, Sequence coverage: 76.2%
    - Total number of restraints: 3344
    - Weight of restraints: 1.0 (3344)
    - Potential type of restraints: upper-bound-parabolic (3344)
    - Range of distance target values: 5.0, 5.1 (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
    - Saveframe: DYANA/DIANA_distance_constraints_3
      - Status: Warning
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 42, Sequence coverage: 9.5%
        Entity_assembly_ID: B, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: C, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: D, Chain length: 42, Sequence coverage: 16.7%
        Entity_assembly_ID: E, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: F, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: G, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: H, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: I, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: J, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: K, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: L, Chain length: 42, Sequence coverage: 26.2%
      - Total number of restraints: 176
        Total hydrogen bond restraints: 176
      - Weight of restraints: 1.0 (176)
        Total hydrogen bond restraints: 1.0 (176)
      - Potential type of restraints: upper-bound-parabolic (176)
        Total hydrogen bond restraints: upper-bound-parabolic (176)
      - Range of distance target values: 1.8, 2.7 (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
      - Saveframe: DYANA/DIANA_distance_constraints_6
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 42, Sequence coverage: 9.5%
        Entity_assembly_ID: B, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: C, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: D, Chain length: 42, Sequence coverage: 16.7%
        Entity_assembly_ID: E, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: F, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: G, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: H, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: I, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: J, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: K, Chain length: 42, Sequence coverage: 26.2%
        Entity_assembly_ID: L, Chain length: 42, Sequence coverage: 26.2%
        Total number of restraints: 176
        Total hydrogen bond restraints: 176
        Weight of restraints: 1.0 (176)
        Total hydrogen bond restraints: 1.0 (176)
        Potential type of restraints: upper-bound-parabolic (176)
        Total hydrogen bond restraints: upper-bound-parabolic (176)
        Range of distance target values: 2.0, 3.0 (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
        Distance restraints on contact map

Keywords Amyloid Fibril, Protein Fibril

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Found 1 Document (3.005 seconds)

BMRB: 25429

Sample

Related entities 1. 42-Residue Beta Amyloid Fibril, : 1 : 44 : 3 : 54 : 18 entities Detail

Interaction partners 1. 42-Residue Beta Amyloid Fibril, : 96 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

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Sample

Instrument

Sample

Instrument

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Instrument

Sample

NMR combined restraints 7 contents Detail